MutSigCV coverage file

[pushpinde...@gmail.com]

Hi,

I want to use MutSigCV and wants to analyze TCGA BRCA samples for mutation analysis. The server said to use coverage file from this path: 

Add Path or URL" under "shared_data/example_files/MutSigCV_1.3/exome_full192.coverage.txt

But when I checked shared_data there is no example_files folder available. Can you please tell from where to get coverage file?

Thanks

Pushpinder

Please respond with the following information as applicable:
 Complete description of the problem (ie what you were trying to do and what went wrong):

Job ID if run on a publicly available server.

If not on Public Server, please share your input files, if possible. If you need to do so privately, let us know.
 
   What were your Parameter values?
   Server Platform (Mac/Linux)?

   Any errors or warnings you see in either stderr.txt, stdout.txt or popup dialogues:


Please note that many common errors can be resolved by searching this forum or taking a look at our documentation: 

* Module Documentation - available from the "documentation" link in the upper right hand corner of the module input page or here: http://software.broadinstitute.org/cancer/software/genepattern/modules
* GenePattern FAQ - http://software.broadinstitute.org/cancer/software/genepattern/FAQ
* GenePattern  Videos - http://software.broadinstitute.org/cancer/software/genepattern/video-tutorials
* GenePattern File Formats - http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#file-formats
* GenePattern User Guide - http://software.broadinstitute.org/cancer/software/genepattern/user-guide#user-guide
* GenePattern Programmer's Guide - http://software.broadinstitute.org/cancer/software/genepattern/programmers-guide
* GenePattern Release Notes - http://software.broadinstitute.org/cancer/software/genepattern/doc/relnotes/current

Please respond with the following information as applicable:
 Complete description of the problem (ie what you were trying to do and what went wrong):

Job ID if run on a publicly available server.

If not on Public Server, please share your input files, if possible. If you need to do so privately, let us know.
 
   What were your Parameter values?
   Server Platform (Mac/Linux)?

   Any errors or warnings you see in either stderr.txt, stdout.txt or popup dialogues:


Please note that many common errors can be resolved by searching this forum or taking a look at our documentation: 

* Module Documentation - available from the "documentation" link in the upper right hand corner of the module input page or here: http://software.broadinstitute.org/cancer/software/genepattern/modules
* GenePattern FAQ - http://software.broadinstitute.org/cancer/software/genepattern/FAQ
* GenePattern  Videos - http://software.broadinstitute.org/cancer/software/genepattern/video-tutorials
* GenePattern File Formats - http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#file-formats
* GenePattern User Guide - http://software.broadinstitute.org/cancer/software/genepattern/user-guide#user-guide
* GenePattern Programmer's Guide - http://software.broadinstitute.org/cancer/software/genepattern/programmers-guide
* GenePattern Release Notes - http://software.broadinstitute.org/cancer/software/genepattern/doc/relnotes/current

[Barbara Hill]

Hello Pushpinder,

Our apologies, the caption for MutSigCV has not been updated since we moved to Amazon.

The file it is referring to can be found here: ftp://gpftp.broadinstitute.org/module_support_files/MutSigCV_1.4/exome_full192.coverage.txt

Please let us know if you have any additional difficulties.

Best

-Barbara

[Александр Несмелов]

Hi! I have similar problem, can't run MutsigCV because the pop-up window opened after clicking 'Add path or URL' button contains only the URL field (see the screenshot attached). Trying both chrome and mozilla did not help, so probably it is not a problem on my side.

I found that this coverage file at some point was stored at 

ftp://gpftp.broadinstitute.org/module_support_files/MutSigCV_1.4/exome_full192.coverage.txt

but now the folder ftp://gpftp.broadinstitute.org/module_support_files/MutSigCV_1.4/ doesn't exist.

Path ftp://gpftp.broadinstitute.org/pub/genepattern/example_files does not seem to contain anything related to mutsigcv as well.

Could you please advise me how to download exome_full192.coverage.txt file or how to enable its choice in the pop-up window?

Kindest regards,

Alex

суббота, 11 мая 2019 г. в 01:05:54 UTC+4, Barbara Hill:

[Ted Liefeld]

Alex,

The Broad institute shut down the ftp site several years ago now.  We have stashed a copy of it in AWS S3 and you should be able to find the MutSigCV files at 

https://datasets.genepattern.org/?prefix=gpftp/module_support_files/MutSigCV_1.4/

and the exon full coverage is there

https://datasets.genepattern.org/gpftp/module_support_files/MutSigCV_1.4/exome_full192.coverage.txt

Please let me know if this solves your problem

Thanks

Ted

[Александр Несмелов]

Yes, it works with this file! 

Thank you so much!

четверг, 4 апреля 2024 г. в 19:25:46 UTC+4, Ted Liefeld: