User: Jeremy Goecks

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Jeremy Goecks2.2k
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j************@emory.edu

Posts by Jeremy Goecks

<prev • 217 results • page 1 of 22 • next >
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Answer: A: Trackster Error Chrom/?.Len , No Such File Or Directory
... You'll need to set your dataset's database/dbkey to your custom reference genome before you can visualize it. We have enhancements planned so that this error doesn't happen in the future. Best, J. ...
written 4.0 years ago by Jeremy Goecks2.2k
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Answer: A: Contents Of A Sam File
... All reads are in the SAM file; you can filter to remove unmapped reads as needed. J. ...
written 4.1 years ago by Jeremy Goecks2.2k
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Comment: C: Re: Galaxy-User Digest, Vol 26, Issue 6
... If you ran Cuffdiff in the last couple months, you used version 2.1.1 ; before that it was 1.3.x The version information was added in the last couple weeks, which is why you don't see it. Any runs going forward should include the version. J. ...
written 4.1 years ago by Jeremy Goecks2.2k
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Answer: A: Trackster Error: Needlargemem: Trying To Allocate 0 Bytes (Limit: 100000000000)
... It turns out that your artificial test is a bit too artificial. In order to display a coverage plot, Trackster converts reads in a BAM to BigWig using a two step process: (1) BAM to bedgraph; (2) bedgraph to bigwig Your super simple example generates an empty file in step 1 because your single rea ...
written 4.1 years ago by Jeremy Goecks2.2k
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Comment: C: Bam Files
... Hello, First, I've moved this question from the Galaxy development mailing list to the Galaxy user mailing list; in the future, please send questions about using Galaxy to the galaxy-user list. To answer your question, files larger than 2GB must be uploaded via FTP to Galaxy. This is necessary due ...
written 4.1 years ago by Jeremy Goecks2.2k
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Answer: A: Problems In Transitioning From Tophat To Cuffdiff
... Are you reporting a bug for each failed Cuffdiff run? That's the easiest way for the Galaxy team to help you out. One thing to keep in mind is that, for now, spaces are not allowed in condition names. We'll address this problem soon. Best, J. ...
written 4.2 years ago by Jeremy Goecks2.2k
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Answer: A: Unable To Import Run Or Save-To-File Published Workflow After Galaxy Upgrade
... Can the workflow's owner view and edit the workflow? My best guess is that you'll need to reinstall some tools that were migrated from the Galaxy framework to the toolshed. See here for details: http://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution J. ...
written 4.2 years ago by Jeremy Goecks2.2k
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Answer: A: Cloudmap
... This sounds an issue with importing workflows. Additional details will help others provide help: (1) What version of Galaxy are you using? (2) What workflow are you trying to import? (3) What steps have you taken that produce the error that you're seeing? Thanks, J. ...
written 4.3 years ago by Jeremy Goecks2.2k
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Answer: A: Cuffdiff Changes
... You can see both the Galaxy tool version and the Cuffdiff tool version (when available) by clicking on the 'view details' icon (the 'i' at the bottom of an expanded dataset). Right now the Cuffdiff version is not displayed, but that will change when our server is updated. That is the version of t ...
written 4.3 years ago by Jeremy Goecks2.2k
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Answer: A: Cuffdiff Changes
... Cuffdiff was recently updated to version 2.1.0; this update likely explains the different results that you see. More samples = more power to accurately estimate expression levels = more DE genes. Replicate data will be available when we next update our server. This should occur in about 3 weeks ...
written 4.3 years ago by Jeremy Goecks2.2k

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