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browser track for Lantermann UTR/ncRNA dataset #62

Open mah11 opened 8 years ago

mah11 commented 8 years ago

Data in spreadsheet attached to Jira PB-2623. Kim may have converted it to GFF at some point already; if not, that's to do.

Datatype: "Curated transcripts" Method: Manually curated from PMID: 18641648 transcriptome data- Strain: h90 WT PMID:20118936

ValWood commented 4 years ago

Do we still have access to this file ?

ValWood commented 4 years ago

moved to https://github.com/pombase/website/issues/1441

mah11 commented 4 years ago

It's GSE16040 in GEO

ValWood commented 4 years ago

I'm looking for the curated transcripts file that was converted to GFF?

kimrutherford commented 4 years ago

I'm looking for the curated transcripts file that was converted to GFF?

We have some files that used to be in Dropbox and are now archived on the server. Do these look right?:

Lantermann_dutrow_utrs_chr1.embl Lanterman_utrs_chr2.embl Lanterman_utrs_chr3.embl original_1.embl original_2.embl original_3.embl utrs-Chr1.embl utrs-Chr2.embl utrs-Chr3.embl

I don't remember converting these to GFF and I can't find any corresponding GFF files.

/data/pombase/archive_from_dropbox/Data/Broad/utrs/

ValWood commented 4 years ago

I have a feeling these might be the files we used to do https://www.pombase.org/faq/how-do-you-determine-gene-s-full-length-transcript-utr-coordinates-transcription-start-and-end-sites

I will try to figure out the difference between the 3 sets in Artemis.... I will also check the format in the paper. This isn't the broad dataset though (as the directory label states) (maybe some of the embl files are the broad and we are only interested here in the ones labelled "Lanterman"

I now remember that we had this data somewhere in a local directory , but I can't remember where that was...

ValWood commented 4 years ago

It might have been under svn, or somewhere on the old Oliver 0. This also might have had the scripts for the file priorities so it might be useful to locate...

ValWood commented 2 years ago

I have been looking for this. @kimrutherford could you have a look at some point. I think this dataset would be useful to align with our curation.

kimrutherford commented 2 years ago

All I can find the files mentioned in this comment: https://github.com/pombase/website/issues/62#issuecomment-671910129=

Do you have any more clues you can give me?

Antonialock commented 2 years ago

Isn’t there a download of everything that was in jira? Maybe search it for pb-2623?

ValWood commented 2 years ago

I haven't had access to Jira since Po-xit. I'll go back to the paper. There are a few papers which mention revised gen annotation sets that I need to dig out and read.

@kimrutherford I will get onto this after the 9th. Assigned to me for now.

kimrutherford commented 2 years ago

Isn’t there a download of everything that was in jira? Maybe search it for pb-2623?

Thanks Antonia! You're right. I had forgotten that we downloaded a copy of the Jira tickets. I've put a copy in Dropbox/pombase/temp/ebi_jira_tickets_backup

They are HTML files. They render OK if you open them in Firefox. These files mention "Lanterman":

jira-2623.html jira-2624.html jira-2003.html jira-1353.html jira-1088.html

These files mention "Dutrow":

jira-2624.html jira-1353.html jira-1088.html jira-1018.html

I've had a look but I can't see any filenames that would help.

Antonialock commented 2 years ago

2623 mentions a file called nsmb.1741-S2.xls

"

This is the other set of manually curated features.(will upload)Its a apreadsheet so it will need converting to gff. I'll assign to Kim first because we used this dataset in the current UTRS (with lower precedence than the Rhind data). I wonder if Kim already did the conversion somewhere. I looked in the UTR files in the drop box, and I could only find EMBL files.

It will appear under "transciptome"

Datatype- "Curated transcripts"Method-Manually curated from PMID: 18641648 transcriptome data-Strain h90 WTcitation PMID: 20118936"

On Thu, Mar 31, 2022 at 10:22 AM Kim Rutherford @.***> wrote:

Isn’t there a download of everything that was in jira? Maybe search it for pb-2623?

Thanks Antonia! You're right. I had forgotten that we downloaded a copy of the Jira tickets. I've put a copy in Dropbox/pombase/temp/ebi_jira_tickets_backup

They are HTML files. They render OK if you open them in Firefox. These files mention "Lanterman":

jira-2623.html jira-2624.html jira-2003.html jira-1353.html jira-1088.html

These files mention "Dutrow":

jira-2624.html jira-1353.html jira-1088.html jira-1018.html

I've had a look but I can't see any filenames that would help.

— Reply to this email directly, view it on GitHub https://github.com/pombase/website/issues/62#issuecomment-1084315273, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADBDJUVPEBZ45WOPNY6TEM3VCVVEXANCNFSM4CNCMWAA . You are receiving this because you were assigned.Message ID: @.***>

Antonialock commented 2 years ago

you might be able to request your username, and then password, using your email if required.. https://www.ebi.ac.uk/panda/jira/browse/PB-2623

I can log in but not see this issue - I think because my pombase account got merged with my new ebi account when I started here & I lost permissions.

On Thu, Mar 31, 2022 at 10:31 AM Antonia Lock @.***> wrote:

2623 mentions a file called nsmb.1741-S2.xls

"

This is the other set of manually curated features.(will upload)Its a apreadsheet so it will need converting to gff. I'll assign to Kim first because we used this dataset in the current UTRS (with lower precedence than the Rhind data). I wonder if Kim already did the conversion somewhere. I looked in the UTR files in the drop box, and I could only find EMBL files.

It will appear under "transciptome"

Datatype- "Curated transcripts"Method-Manually curated from PMID: 18641648 transcriptome data-Strain h90 WTcitation PMID: 20118936"

On Thu, Mar 31, 2022 at 10:22 AM Kim Rutherford @.***> wrote:

Isn’t there a download of everything that was in jira? Maybe search it for pb-2623?

Thanks Antonia! You're right. I had forgotten that we downloaded a copy of the Jira tickets. I've put a copy in Dropbox/pombase/temp/ebi_jira_tickets_backup

They are HTML files. They render OK if you open them in Firefox. These files mention "Lanterman":

jira-2623.html jira-2624.html jira-2003.html jira-1353.html jira-1088.html

These files mention "Dutrow":

jira-2624.html jira-1353.html jira-1088.html jira-1018.html

I've had a look but I can't see any filenames that would help.

— Reply to this email directly, view it on GitHub https://github.com/pombase/website/issues/62#issuecomment-1084315273, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADBDJUVPEBZ45WOPNY6TEM3VCVVEXANCNFSM4CNCMWAA . You are receiving this because you were assigned.Message ID: @.***>

kimrutherford commented 2 years ago

Thanks again Antonia. You're good at this. :-)

kimrutherford commented 2 years ago

Sorry, hit return too quick

2623 mentions a file called nsmb.1741-S2.xls

I think that must be S2 of: https://www.nature.com/articles/nsmb.1741

ValWood commented 11 months ago

I woud quite like to be abe to view this dataset in the New Year for the genome update paper. I'd like to compare to the curated transcripts

kimrutherford commented 11 months ago

OK, let's chat about this soon. I have questions about the dataset.