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UCSC doesn't support non alphanumeric chromosome names #100

Closed cadley-nyulangone closed 4 years ago

cadley-nyulangone commented 4 years ago

As an example:

Go to cegsvectors and then Sox2_Sox2_143kb~marker_backbone

Then do View -> PDF/PS

An error message appears. This happens for all sequence names containing a tilde.

cadley-nyulangone commented 4 years ago

UCSC says that tilde is not available for use in sequence names.

From: Daniel Schmelter 
Date: Thu, Nov 14, 2019 at 6:25 PM
Subject: Re: [genome] Browser Graphic Names
To: John Cadley 
Cc: UCSC Genome Browser Discussion List 

Hello John,

Thank you for your question about tilde characters in sequence names.

The tilde character(~) is not currently available for use in sequence names and will probably not add support for that character unless there is significant demand. These types of unusual characters can sometimes interfere with our position parsing and it would probably be best to stick to more standard characters. Thank you again for reporting your issue.

If you have any further questions, please reply to genome@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genome-www@soe.ucsc.edu.

Kindly,
Daniel Schmelter
UCSC Genome Browser
mattmaurano commented 4 years ago

John, can you get a complete list of valid characters in chromosome names?

cadley-nyulangone commented 4 years ago

Will do

On Wed, Nov 20, 2019, 11:35 AM mattmaurano notifications@github.com wrote:

John, can you get a complete list of valid characters in chromosome names?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/mauranolab/mapping/issues/100?email_source=notifications&email_token=AKY4NJUXRWWDZQOZVXFFGYDQUVRMPA5CNFSM4JL37DBKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEESTZYA#issuecomment-556088544, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKY4NJQZKX5WICRGSN6XQY3QUVRMPANCNFSM4JL37DBA .

cadley-nyulangone commented 4 years ago

From UCSC:

The allowed character set for sequence names includes upper-case letters, lower-case letters, numbers, underscores, and dashes. This can also be expressed as:

  [A-Za-z_0-9_-]

I added a note about that to our Track Hub documentation page:

  http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Setup

On Wed, Nov 20, 2019 at 12:20 PM John Cadley cadley.nyulangone@gmail.com wrote:

Will do

On Wed, Nov 20, 2019, 11:35 AM mattmaurano notifications@github.com wrote:

John, can you get a complete list of valid characters in chromosome names?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/mauranolab/mapping/issues/100?email_source=notifications&email_token=AKY4NJUXRWWDZQOZVXFFGYDQUVRMPA5CNFSM4JL37DBKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEESTZYA#issuecomment-556088544, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKY4NJQZKX5WICRGSN6XQY3QUVRMPANCNFSM4JL37DBA .

mattmaurano commented 4 years ago

OK, got it. Where did you add a note?

We will substitute illegal character names in chromosome names with an underscore; the assembly name will stay the same. I've updated makeCustomReference.sh to do this.

Can you make a list of the samples in /vol/cegs/mapped that used these references? It will need to be reprocessed. cegsvectors_HTRA1_LIMS1_CPA~URA cegsvectors_IRF5_103K~Assembly_URA~Swapin cegsvectors_Sox2_Sox2_143kb~marker cegsvectors_Sox2_Sox2_46kb~dDistalLCR~marker

--Matt

On Nov 20, 2019, at 3:03 PM, cadley-nyulangone notifications@github.com wrote:

From UCSC:

The allowed character set for sequence names includes upper-case letters, lower-case letters, numbers, underscores, and dashes. This can also be expressed as:

[A-Za-z0-9-]

I added a note about that to our Track Hub documentation page:

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Setup

On Wed, Nov 20, 2019 at 12:20 PM John Cadley cadley.nyulangone@gmail.com wrote:

Will do

On Wed, Nov 20, 2019, 11:35 AM mattmaurano notifications@github.com wrote:

John, can you get a complete list of valid characters in chromosome names?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/mauranolab/mapping/issues/100?email_source=notifications&email_token=AKY4NJUXRWWDZQOZVXFFGYDQUVRMPA5CNFSM4JL37DBKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEESTZYA#issuecomment-556088544, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKY4NJQZKX5WICRGSN6XQY3QUVRMPANCNFSM4JL37DBA .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

cadley-nyulangone commented 4 years ago

FCHC7T7BGXB /vol/cegs/mapped/FCHC7T7BGXB/submitJobs.FCHC7T7BGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_A05 BS02838A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C02 BS02839A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C03 BS02840A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C04 BS02841A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C10 BS02842A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_D09 BS02843A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F01 BS02844A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F05 BS02845A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F11 BS02846A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_G02 BS02847A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_G03 BS02848A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_H03 BS02849A

FCHF7N3BGXB /vol/cegs/mapped/FCHF7N3BGXB/submitJobs.FCHF7N3BGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B1_Yeast BS02937A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B2_Yeast BS02938A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B3_Yeast BS02939A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B4_Yeast BS02940A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B5_Yeast BS02941A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B6_Yeast BS02942A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D1_Yeast BS02943A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D2_Yeast BS02944A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D3_Yeast BS02945A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D4_Yeast BS02946A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D5_Yeast BS02947A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D6_Yeast BS02948A

FCHVGHLBGXB /vol/cegs/mapped/FCHVGHLBGXB/submitJobs.FCHVGHLBGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_Sox2_Sox2_46kb~dDistalLCR~marker,mm10 mapBwaMem,dna dna/Sox2_Sox2_46kb~dDistalLCR~marker_BAC BS03435A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_Sox2_Sox2_143kb~marker,mm10 mapBwaMem,dna dna/Sox2_Sox2_143kb~marker_BAC BS03436A

============================================================================================================================================= The reference to the note was from the UCSC email to me. They were just saying that they updated their website. It looks like this now:

To create your own hub you will need:

John

On Wed, Nov 20, 2019 at 3:20 PM mattmaurano notifications@github.com wrote:

OK, got it. Where did you add a note?

We will substitute illegal character names in chromosome names with an underscore; the assembly name will stay the same. I've updated makeCustomReference.sh to do this.

Can you make a list of the samples in /vol/cegs/mapped that used these references? It will need to be reprocessed. cegsvectors_HTRA1_LIMS1_CPA~URA cegsvectors_IRF5_103K~Assembly_URA~Swapin cegsvectors_Sox2_Sox2_143kb~marker cegsvectors_Sox2_Sox2_46kb~dDistalLCR~marker

--Matt

On Nov 20, 2019, at 3:03 PM, cadley-nyulangone notifications@github.com wrote:

From UCSC:

The allowed character set for sequence names includes upper-case letters, lower-case letters, numbers, underscores, and dashes. This can also be expressed as:

[A-Za-z0-9-]

I added a note about that to our Track Hub documentation page:

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Setup

On Wed, Nov 20, 2019 at 12:20 PM John Cadley < cadley.nyulangone@gmail.com> wrote:

Will do

On Wed, Nov 20, 2019, 11:35 AM mattmaurano notifications@github.com wrote:

John, can you get a complete list of valid characters in chromosome names?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub < https://github.com/mauranolab/mapping/issues/100?email_source=notifications&email_token=AKY4NJUXRWWDZQOZVXFFGYDQUVRMPA5CNFSM4JL37DBKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEESTZYA#issuecomment-556088544 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AKY4NJQZKX5WICRGSN6XQY3QUVRMPANCNFSM4JL37DBA

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/mauranolab/mapping/issues/100?email_source=notifications&email_token=AKY4NJSPQJSRHDHGMRFYMRDQUWLZHA5CNFSM4JL37DBKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEUSABI#issuecomment-556343301, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKY4NJTMCFQHN3MBY5AJHJ3QUWLZHANCNFSM4JL37DBA .

mattmaurano commented 4 years ago

Can you get me the directory names in the same format as last time?

--Matt

On Nov 20, 2019, at 4:02 PM, cadley-nyulangone notifications@github.com wrote:

FCHC7T7BGXB /vol/cegs/mapped/FCHC7T7BGXB/submitJobs.FCHC7T7BGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_A05 BS02838A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C02 BS02839A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C03 BS02840A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C04 BS02841A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C10 BS02842A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_D09 BS02843A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F01 BS02844A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F05 BS02845A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F11 BS02846A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_G02 BS02847A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_G03 BS02848A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_H03 BS02849A

FCHF7N3BGXB /vol/cegs/mapped/FCHF7N3BGXB/submitJobs.FCHF7N3BGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B1_Yeast BS02937A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B2_Yeast BS02938A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B3_Yeast BS02939A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B4_Yeast BS02940A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B5_Yeast BS02941A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B6_Yeast BS02942A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D1_Yeast BS02943A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D2_Yeast BS02944A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D3_Yeast BS02945A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D4_Yeast BS02946A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D5_Yeast BS02947A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D6_Yeast BS02948A

FCHVGHLBGXB /vol/cegs/mapped/FCHVGHLBGXB/submitJobs.FCHVGHLBGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_Sox2_Sox2_46kb~dDistalLCR~marker,mm10 mapBwaMem,dna dna/Sox2_Sox2_46kb~dDistalLCR~marker_BAC BS03435A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_Sox2_Sox2_143kb~marker,mm10 mapBwaMem,dna dna/Sox2_Sox2_143kb~marker_BAC BS03436A

============================================================================================================================================= The reference to the note was from the UCSC email to me. They were just saying that they updated their website. It looks like this now:

To create your own hub you will need:

  • one or more data sets formatted in one of the compressed binary index formats supported by the Genome Browser: bigBed, bigBarChart, bigGenePred, bigNarrowPeak, bigPsl, bigChain, bigInteract, bigMaf, bigWig, BAM, CRAM, HAL, hic or VCF
  • a set of text files that specify properties for the track hub and for each of the data tracks within it
  • a twoBit file with your sequence if you are setting up an assembly hub. Note that the allowed characters in sequence names are [A-Za-z0-9-]
  • an Internet-enabled web server or ftp server

John

On Wed, Nov 20, 2019 at 3:20 PM mattmaurano notifications@github.com wrote:

OK, got it. Where did you add a note?

We will substitute illegal character names in chromosome names with an underscore; the assembly name will stay the same. I've updated makeCustomReference.sh to do this.

Can you make a list of the samples in /vol/cegs/mapped that used these references? It will need to be reprocessed. cegsvectors_HTRA1_LIMS1_CPA~URA cegsvectors_IRF5_103K~Assembly_URA~Swapin cegsvectors_Sox2_Sox2_143kb~marker cegsvectors_Sox2_Sox2_46kb~dDistalLCR~marker

--Matt

On Nov 20, 2019, at 3:03 PM, cadley-nyulangone notifications@github.com wrote:

From UCSC:

The allowed character set for sequence names includes upper-case letters, lower-case letters, numbers, underscores, and dashes. This can also be expressed as:

[A-Za-z0-9-]

I added a note about that to our Track Hub documentation page:

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Setup

On Wed, Nov 20, 2019 at 12:20 PM John Cadley < cadley.nyulangone@gmail.com> wrote:

Will do

On Wed, Nov 20, 2019, 11:35 AM mattmaurano notifications@github.com wrote:

John, can you get a complete list of valid characters in chromosome names?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub < https://github.com/mauranolab/mapping/issues/100?email_source=notifications&email_token=AKY4NJUXRWWDZQOZVXFFGYDQUVRMPA5CNFSM4JL37DBKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEESTZYA#issuecomment-556088544 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AKY4NJQZKX5WICRGSN6XQY3QUVRMPANCNFSM4JL37DBA

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

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cadley-nyulangone commented 4 years ago

/vol/cegs/mapped/FCHVGHLBGXB/dna/Sox2_Sox2_143kb~marker_BAC-BS03436A /vol/cegs/mapped/FCHVGHLBGXB/dna/Sox2_Sox2_46kb~dDistalLCR~marker_BAC-BS03435A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B1_Yeast-BS02937A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B2_Yeast-BS02938A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B3_Yeast-BS02939A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B4_Yeast-BS02940A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B5_Yeast-BS02941A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B6_Yeast-BS02942A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D1_Yeast-BS02943A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D2_Yeast-BS02944A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D3_Yeast-BS02945A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D4_Yeast-BS02946A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D5_Yeast-BS02947A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D6_Yeast-BS02948A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_A05-BS02838A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_C02-BS02839A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_C03-BS02840A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_C04-BS02841A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_C10-BS02842A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_D09-BS02843A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_F01-BS02844A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_F05-BS02845A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_F11-BS02846A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_G02-BS02847A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_G03-BS02848A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_H03-BS02849A

John

On Wed, Nov 20, 2019 at 4:04 PM mattmaurano notifications@github.com wrote:

Can you get me the directory names in the same format as last time?

--Matt

On Nov 20, 2019, at 4:02 PM, cadley-nyulangone notifications@github.com wrote:

FCHC7T7BGXB /vol/cegs/mapped/FCHC7T7BGXB/submitJobs.FCHC7T7BGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_A05 BS02838A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C02 BS02839A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C03 BS02840A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C04 BS02841A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C10 BS02842A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_D09 BS02843A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F01 BS02844A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F05 BS02845A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F11 BS02846A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_G02 BS02847A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_G03 BS02848A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_H03 BS02849A

FCHF7N3BGXB /vol/cegs/mapped/FCHF7N3BGXB/submitJobs.FCHF7N3BGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B1_Yeast BS02937A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B2_Yeast BS02938A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B3_Yeast BS02939A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B4_Yeast BS02940A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B5_Yeast BS02941A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B6_Yeast BS02942A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D1_Yeast BS02943A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D2_Yeast BS02944A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D3_Yeast BS02945A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D4_Yeast BS02946A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D5_Yeast BS02947A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D6_Yeast BS02948A

FCHVGHLBGXB /vol/cegs/mapped/FCHVGHLBGXB/submitJobs.FCHVGHLBGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_Sox2_Sox2_46kb~dDistalLCR~marker,mm10 mapBwaMem,dna dna/Sox2_Sox2_46kb~dDistalLCR~marker_BAC BS03435A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_Sox2_Sox2_143kb~marker,mm10 mapBwaMem,dna dna/Sox2_Sox2_143kb~marker_BAC BS03436A

============================================================================================================================================= The reference to the note was from the UCSC email to me. They were just saying that they updated their website. It looks like this now:

To create your own hub you will need:

  • one or more data sets formatted in one of the compressed binary index formats supported by the Genome Browser: bigBed, bigBarChart, bigGenePred, bigNarrowPeak, bigPsl, bigChain, bigInteract, bigMaf, bigWig, BAM, CRAM, HAL, hic or VCF
  • a set of text files that specify properties for the track hub and for each of the data tracks within it
  • a twoBit file with your sequence if you are setting up an assembly hub. Note that the allowed characters in sequence names are [A-Za-z0-9-]
  • an Internet-enabled web server or ftp server

John

On Wed, Nov 20, 2019 at 3:20 PM mattmaurano notifications@github.com wrote:

OK, got it. Where did you add a note?

We will substitute illegal character names in chromosome names with an underscore; the assembly name will stay the same. I've updated makeCustomReference.sh to do this.

Can you make a list of the samples in /vol/cegs/mapped that used these references? It will need to be reprocessed. cegsvectors_HTRA1_LIMS1_CPA~URA cegsvectors_IRF5_103K~Assembly_URA~Swapin cegsvectors_Sox2_Sox2_143kb~marker cegsvectors_Sox2_Sox2_46kb~dDistalLCR~marker

--Matt

On Nov 20, 2019, at 3:03 PM, cadley-nyulangone < notifications@github.com> wrote:

From UCSC:

The allowed character set for sequence names includes upper-case letters, lower-case letters, numbers, underscores, and dashes. This can also be expressed as:

[A-Za-z0-9-]

I added a note about that to our Track Hub documentation page:

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Setup

On Wed, Nov 20, 2019 at 12:20 PM John Cadley < cadley.nyulangone@gmail.com> wrote:

Will do

On Wed, Nov 20, 2019, 11:35 AM mattmaurano < notifications@github.com> wrote:

John, can you get a complete list of valid characters in chromosome names?

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mattmaurano commented 4 years ago

Thanks

Can you refresh the dev hub and make sure everything loads and the issues are fixed?

--Matt

On Nov 20, 2019, at 4:23 PM, cadley-nyulangone notifications@github.com wrote:

/vol/cegs/mapped/FCHVGHLBGXB/dna/Sox2_Sox2_143kb~marker_BAC-BS03436A /vol/cegs/mapped/FCHVGHLBGXB/dna/Sox2_Sox2_46kb~dDistalLCR~marker_BAC-BS03435A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B1_Yeast-BS02937A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B2_Yeast-BS02938A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B3_Yeast-BS02939A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B4_Yeast-BS02940A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B5_Yeast-BS02941A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B6_Yeast-BS02942A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D1_Yeast-BS02943A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D2_Yeast-BS02944A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D3_Yeast-BS02945A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D4_Yeast-BS02946A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D5_Yeast-BS02947A /vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D6_Yeast-BS02948A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_A05-BS02838A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_C02-BS02839A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_C03-BS02840A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_C04-BS02841A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_C10-BS02842A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_D09-BS02843A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_F01-BS02844A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_F05-BS02845A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_F11-BS02846A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_G02-BS02847A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_G03-BS02848A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_H03-BS02849A

John

On Wed, Nov 20, 2019 at 4:04 PM mattmaurano notifications@github.com wrote:

Can you get me the directory names in the same format as last time?

--Matt

On Nov 20, 2019, at 4:02 PM, cadley-nyulangone notifications@github.com wrote:

FCHC7T7BGXB /vol/cegs/mapped/FCHC7T7BGXB/submitJobs.FCHC7T7BGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_A05 BS02838A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C02 BS02839A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C03 BS02840A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C04 BS02841A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C10 BS02842A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_D09 BS02843A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F01 BS02844A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F05 BS02845A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F11 BS02846A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_G02 BS02847A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_G03 BS02848A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_H03 BS02849A

FCHF7N3BGXB /vol/cegs/mapped/FCHF7N3BGXB/submitJobs.FCHF7N3BGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B1_Yeast BS02937A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B2_Yeast BS02938A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B3_Yeast BS02939A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B4_Yeast BS02940A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B5_Yeast BS02941A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B6_Yeast BS02942A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D1_Yeast BS02943A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D2_Yeast BS02944A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D3_Yeast BS02945A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D4_Yeast BS02946A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D5_Yeast BS02947A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D6_Yeast BS02948A

FCHVGHLBGXB /vol/cegs/mapped/FCHVGHLBGXB/submitJobs.FCHVGHLBGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_Sox2_Sox2_46kb~dDistalLCR~marker,mm10 mapBwaMem,dna dna/Sox2_Sox2_46kb~dDistalLCR~marker_BAC BS03435A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_Sox2_Sox2_143kb~marker,mm10 mapBwaMem,dna dna/Sox2_Sox2_143kb~marker_BAC BS03436A

============================================================================================================================================= The reference to the note was from the UCSC email to me. They were just saying that they updated their website. It looks like this now:

To create your own hub you will need:

  • one or more data sets formatted in one of the compressed binary index formats supported by the Genome Browser: bigBed, bigBarChart, bigGenePred, bigNarrowPeak, bigPsl, bigChain, bigInteract, bigMaf, bigWig, BAM, CRAM, HAL, hic or VCF
  • a set of text files that specify properties for the track hub and for each of the data tracks within it
  • a twoBit file with your sequence if you are setting up an assembly hub. Note that the allowed characters in sequence names are [A-Za-z0-9-]
  • an Internet-enabled web server or ftp server

John

On Wed, Nov 20, 2019 at 3:20 PM mattmaurano notifications@github.com wrote:

OK, got it. Where did you add a note?

We will substitute illegal character names in chromosome names with an underscore; the assembly name will stay the same. I've updated makeCustomReference.sh to do this.

Can you make a list of the samples in /vol/cegs/mapped that used these references? It will need to be reprocessed. cegsvectors_HTRA1_LIMS1_CPA~URA cegsvectors_IRF5_103K~Assembly_URA~Swapin cegsvectors_Sox2_Sox2_143kb~marker cegsvectors_Sox2_Sox2_46kb~dDistalLCR~marker

--Matt

On Nov 20, 2019, at 3:03 PM, cadley-nyulangone < notifications@github.com> wrote:

From UCSC:

The allowed character set for sequence names includes upper-case letters, lower-case letters, numbers, underscores, and dashes. This can also be expressed as:

[A-Za-z0-9-]

I added a note about that to our Track Hub documentation page:

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Setup

On Wed, Nov 20, 2019 at 12:20 PM John Cadley < cadley.nyulangone@gmail.com> wrote:

Will do

On Wed, Nov 20, 2019, 11:35 AM mattmaurano < notifications@github.com> wrote:

John, can you get a complete list of valid characters in chromosome names?

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cadley-nyulangone commented 4 years ago

I just refreshed dev.

I can see the sequences for the 2 Sox2 line items, and View -> PDF/PS works.

When I go to View -> PDF/PS for the others, I don't get the error message that used to appear.

However, there is no bed file for these other sequences, so there is nothing to look at except for the whatever flowcell tracks appear in that region.

John

On Wed, Nov 20, 2019 at 10:20 PM mattmaurano notifications@github.com wrote:

Thanks

Can you refresh the dev hub and make sure everything loads and the issues are fixed?

--Matt

On Nov 20, 2019, at 4:23 PM, cadley-nyulangone notifications@github.com wrote:

/vol/cegs/mapped/FCHVGHLBGXB/dna/Sox2_Sox2_143kb~marker_BAC-BS03436A

/vol/cegs/mapped/FCHVGHLBGXB/dna/Sox2_Sox2_46kb~dDistalLCR~marker_BAC-BS03435A

/vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B1_Yeast-BS02937A

/vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B2_Yeast-BS02938A

/vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B3_Yeast-BS02939A

/vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B4_Yeast-BS02940A

/vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B5_Yeast-BS02941A

/vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Big~B6_Yeast-BS02942A

/vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D1_Yeast-BS02943A

/vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D2_Yeast-BS02944A

/vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D3_Yeast-BS02945A

/vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D4_Yeast-BS02946A

/vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D5_Yeast-BS02947A

/vol/cegs/mapped/FCHF7N3BGXB/dna/IRF5_103K~Assembly_URA~Swapin_Small~D6_Yeast-BS02948A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_A05-BS02838A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_C02-BS02839A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_C03-BS02840A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_C04-BS02841A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_C10-BS02842A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_D09-BS02843A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_F01-BS02844A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_F05-BS02845A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_F11-BS02846A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_G02-BS02847A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_G03-BS02848A /vol/cegs/mapped/FCHC7T7BGXB/dna/HTRA1_LIMS1_CPA~URA_H03-BS02849A

John

On Wed, Nov 20, 2019 at 4:04 PM mattmaurano notifications@github.com wrote:

Can you get me the directory names in the same format as last time?

--Matt

On Nov 20, 2019, at 4:02 PM, cadley-nyulangone < notifications@github.com> wrote:

FCHC7T7BGXB /vol/cegs/mapped/FCHC7T7BGXB/submitJobs.FCHC7T7BGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_A05 BS02838A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C02 BS02839A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C03 BS02840A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C04 BS02841A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_C10 BS02842A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_D09 BS02843A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F01 BS02844A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F05 BS02845A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_F11 BS02846A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_G02 BS02847A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_G03 BS02848A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_HTRA1_LIMS1_CPA~URA,hg38_sacCer3 mapBwaMem,dna dna/HTRA1_LIMS1_CPA~URA_H03 BS02849A

FCHF7N3BGXB /vol/cegs/mapped/FCHF7N3BGXB/submitJobs.FCHF7N3BGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B1_Yeast BS02937A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B2_Yeast BS02938A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B3_Yeast BS02939A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B4_Yeast BS02940A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B5_Yeast BS02941A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Big~B6_Yeast BS02942A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D1_Yeast BS02943A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D2_Yeast BS02944A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D3_Yeast BS02945A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D4_Yeast BS02946A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D5_Yeast BS02947A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_IRF5_103K~Assembly_URA~Swapin,hg38_sacCer3 mapBwaMem,dna dna/IRF5_103K~Assembly_URA~Swapin_Small~D6_Yeast BS02948A

FCHVGHLBGXB /vol/cegs/mapped/FCHVGHLBGXB/submitJobs.FCHVGHLBGXB.Project_CEGS.sh /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_Sox2_Sox2_46kb~dDistalLCR~marker,mm10 mapBwaMem,dna dna/Sox2_Sox2_46kb~dDistalLCR~marker_BAC BS03435A /vol/mauranolab/mapped/src/dnase/submit.sh cegsvectors_Sox2_Sox2_143kb~marker,mm10 mapBwaMem,dna dna/Sox2_Sox2_143kb~marker_BAC BS03436A

=============================================================================================================================================

The reference to the note was from the UCSC email to me. They were just saying that they updated their website. It looks like this now:

To create your own hub you will need:

  • one or more data sets formatted in one of the compressed binary index formats supported by the Genome Browser: bigBed, bigBarChart, bigGenePred, bigNarrowPeak, bigPsl, bigChain, bigInteract, bigMaf, bigWig, BAM, CRAM, HAL, hic or VCF
  • a set of text files that specify properties for the track hub and for each of the data tracks within it
  • a twoBit file with your sequence if you are setting up an assembly hub. Note that the allowed characters in sequence names are [A-Za-z0-9-]
  • an Internet-enabled web server or ftp server

John

On Wed, Nov 20, 2019 at 3:20 PM mattmaurano < notifications@github.com> wrote:

OK, got it. Where did you add a note?

We will substitute illegal character names in chromosome names with an underscore; the assembly name will stay the same. I've updated makeCustomReference.sh to do this.

Can you make a list of the samples in /vol/cegs/mapped that used these references? It will need to be reprocessed. cegsvectors_HTRA1_LIMS1_CPA~URA cegsvectors_IRF5_103K~Assembly_URA~Swapin cegsvectors_Sox2_Sox2_143kb~marker cegsvectors_Sox2_Sox2_46kb~dDistalLCR~marker

--Matt

On Nov 20, 2019, at 3:03 PM, cadley-nyulangone < notifications@github.com> wrote:

From UCSC:

The allowed character set for sequence names includes upper-case letters, lower-case letters, numbers, underscores, and dashes. This can also be expressed as:

[A-Za-z0-9-]

I added a note about that to our Track Hub documentation page:

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Setup

On Wed, Nov 20, 2019 at 12:20 PM John Cadley < cadley.nyulangone@gmail.com> wrote:

Will do

On Wed, Nov 20, 2019, 11:35 AM mattmaurano < notifications@github.com> wrote:

John, can you get a complete list of valid characters in chromosome names?

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mattmaurano commented 4 years ago

OK, then revise the title of this issue to better reflect the problem and close it.

Then refresh the main and reply to my email from yesterday so Ran et al know it's fixed