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jandrewrfarrell / RUFUS

RUFUS k-mer based genomic variant detection
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manual #2

Open galapah opened 8 years ago

galapah commented 8 years ago

Hello,

I am keen on trying this tool on our data! I already have kmers calculated by Jellyfish. However, I am not sure how to proceed further. Can you please provide at least a sample sequence of commands?

Jan

jandrewrfarrell commented 8 years ago

This project is still under development, but you will find script files that should run everything in RUFUS/scripts/. RunRUFUS.HumanTrio.sh should run a trio analysis start to finish. What type of experiment are you trying to run ?

On Thu, Jun 16, 2016 at 1:47 PM, galapah notifications@github.com wrote:

Hello,

I am keen on trying this tool on our data! I already have kmers calculated by Jellyfish. However, I am not sure how to proceed next. Can you please provide at least a sample sequence of commands?

Jan

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jandrewrfarrell/RUFUS/issues/2, or mute the thread https://github.com/notifications/unsubscribe/AGVbHjRjJvEk9HLmY_E4ukQz4JKg1yR_ks5qMahMgaJpZM4I3vUC .

galapah commented 8 years ago

Hi,

thank you for quick response! I am sorry, I cannot see the RunRUFUS.HumanTrio.sh http://runrufus.humantrio.sh/ even on GitHub: https://github.com/jandrewrfarrell/RUFUS/tree/master/scripts

I have reads from two plant individuals (mutant vs wildtype).

Jan

2016-06-16 22:11 GMT+02:00 J Andrew R Farrell notifications@github.com:

This project is still under development, but you will find script files that should run everything in RUFUS/scripts/. RunRUFUS.HumanTrio.sh should run a trio analysis start to finish. What type of experiment are you trying to run ?

On Thu, Jun 16, 2016 at 1:47 PM, galapah notifications@github.com wrote:

Hello,

I am keen on trying this tool on our data! I already have kmers calculated by Jellyfish. However, I am not sure how to proceed next. Can you please provide at least a sample sequence of commands?

Jan

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jandrewrfarrell/RUFUS/issues/2, or mute the thread < https://github.com/notifications/unsubscribe/AGVbHjRjJvEk9HLmY_E4ukQz4JKg1yR_ks5qMahMgaJpZM4I3vUC

.

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galapah commented 8 years ago

I am running scripts/RunTumor.sh now.

2016-06-16 22:23 GMT+02:00 Jan Hapala jan@hapala.cz:

Hi,

thank you for quick response! I am sorry, I cannot see the RunRUFUS.HumanTrio.sh http://runrufus.humantrio.sh/ even on GitHub: https://github.com/jandrewrfarrell/RUFUS/tree/master/scripts

I have reads from two plant individuals (mutant vs wildtype).

Jan

2016-06-16 22:11 GMT+02:00 J Andrew R Farrell notifications@github.com:

This project is still under development, but you will find script files that should run everything in RUFUS/scripts/. RunRUFUS.HumanTrio.sh should run a trio analysis start to finish. What type of experiment are you trying to run ?

On Thu, Jun 16, 2016 at 1:47 PM, galapah notifications@github.com wrote:

Hello,

I am keen on trying this tool on our data! I already have kmers calculated by Jellyfish. However, I am not sure how to proceed next. Can you please provide at least a sample sequence of commands?

Jan

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jandrewrfarrell/RUFUS/issues/2, or mute the thread < https://github.com/notifications/unsubscribe/AGVbHjRjJvEk9HLmY_E4ukQz4JKg1yR_ks5qMahMgaJpZM4I3vUC

.

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jandrewrfarrell commented 8 years ago

yeah, tumor normal is what you should use for mutant vs wild type

On Thu, Jun 16, 2016 at 2:36 PM, galapah notifications@github.com wrote:

I am running scripts/RunTumor.sh now.

2016-06-16 22:23 GMT+02:00 Jan Hapala jan@hapala.cz:

Hi,

thank you for quick response! I am sorry, I cannot see the RunRUFUS.HumanTrio.sh http://runrufus.humantrio.sh/ even on GitHub: https://github.com/jandrewrfarrell/RUFUS/tree/master/scripts

I have reads from two plant individuals (mutant vs wildtype).

Jan

2016-06-16 22:11 GMT+02:00 J Andrew R Farrell <notifications@github.com :

This project is still under development, but you will find script files that should run everything in RUFUS/scripts/. RunRUFUS.HumanTrio.sh should run a trio analysis start to finish. What type of experiment are you trying to run ?

On Thu, Jun 16, 2016 at 1:47 PM, galapah notifications@github.com wrote:

Hello,

I am keen on trying this tool on our data! I already have kmers calculated by Jellyfish. However, I am not sure how to proceed next. Can you please provide at least a sample sequence of commands?

Jan

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jandrewrfarrell/RUFUS/issues/2, or mute the thread <

https://github.com/notifications/unsubscribe/AGVbHjRjJvEk9HLmY_E4ukQz4JKg1yR_ks5qMahMgaJpZM4I3vUC

.

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jandrewrfarrell commented 8 years ago

do you have a reference for the plant your using? If so you will need to change that in OverlapBashMultithread.sh to get a VCF. if you don't you just want the mutant contigs you are all set

On Thu, Jun 16, 2016 at 2:45 PM, Andrew Farrell jandrewrfarrell@gmail.com wrote:

yeah, tumor normal is what you should use for mutant vs wild type

On Thu, Jun 16, 2016 at 2:36 PM, galapah notifications@github.com wrote:

I am running scripts/RunTumor.sh now.

2016-06-16 22:23 GMT+02:00 Jan Hapala jan@hapala.cz:

Hi,

thank you for quick response! I am sorry, I cannot see the RunRUFUS.HumanTrio.sh http://runrufus.humantrio.sh/ even on GitHub: https://github.com/jandrewrfarrell/RUFUS/tree/master/scripts

I have reads from two plant individuals (mutant vs wildtype).

Jan

2016-06-16 22:11 GMT+02:00 J Andrew R Farrell <notifications@github.com :

This project is still under development, but you will find script files that should run everything in RUFUS/scripts/. RunRUFUS.HumanTrio.sh should run a trio analysis start to finish. What type of experiment are you trying to run ?

On Thu, Jun 16, 2016 at 1:47 PM, galapah notifications@github.com wrote:

Hello,

I am keen on trying this tool on our data! I already have kmers calculated by Jellyfish. However, I am not sure how to proceed next. Can you please provide at least a sample sequence of commands?

Jan

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jandrewrfarrell/RUFUS/issues/2, or mute the thread <

https://github.com/notifications/unsubscribe/AGVbHjRjJvEk9HLmY_E4ukQz4JKg1yR_ks5qMahMgaJpZM4I3vUC

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galapah commented 8 years ago

Great! Thank your for the tips! It's Arabidopsis so I have a reference.

2016-06-16 22:46 GMT+02:00 J Andrew R Farrell notifications@github.com:

do you have a reference for the plant your using? If so you will need to change that in OverlapBashMultithread.sh to get a VCF. if you don't you just want the mutant contigs you are all set

On Thu, Jun 16, 2016 at 2:45 PM, Andrew Farrell <jandrewrfarrell@gmail.com

wrote:

yeah, tumor normal is what you should use for mutant vs wild type

On Thu, Jun 16, 2016 at 2:36 PM, galapah notifications@github.com wrote:

I am running scripts/RunTumor.sh now.

2016-06-16 22:23 GMT+02:00 Jan Hapala jan@hapala.cz:

Hi,

thank you for quick response! I am sorry, I cannot see the RunRUFUS.HumanTrio.sh http://runrufus.humantrio.sh/ even on GitHub: https://github.com/jandrewrfarrell/RUFUS/tree/master/scripts

I have reads from two plant individuals (mutant vs wildtype).

Jan

2016-06-16 22:11 GMT+02:00 J Andrew R Farrell < notifications@github.com :

This project is still under development, but you will find script files that should run everything in RUFUS/scripts/. RunRUFUS.HumanTrio.sh should run a trio analysis start to finish. What type of experiment are you trying to run ?

On Thu, Jun 16, 2016 at 1:47 PM, galapah notifications@github.com wrote:

Hello,

I am keen on trying this tool on our data! I already have kmers calculated by Jellyfish. However, I am not sure how to proceed next. Can you please provide at least a sample sequence of commands?

Jan

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jandrewrfarrell/RUFUS/issues/2, or mute the thread <

https://github.com/notifications/unsubscribe/AGVbHjRjJvEk9HLmY_E4ukQz4JKg1yR_ks5qMahMgaJpZM4I3vUC

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https://github.com/jandrewrfarrell/RUFUS/issues/2#issuecomment-226599664

,

or mute the thread <

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