Question: (Closed) cummeRbund SQLite database error from Galaxy main CuffDiff tool
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nevil • 20 wrote:
I'm trying to create an SQLite database to download and use with cummeRbund by using the "Create SQLite database" option with Cuffdiff on the main Galaxy instance. However, when this option is selected, the run "fails" though all the other tabular output files seem to still be generated (SQLite db file is empty). Normally, when I have run the same data through Cuffdiff, but do not select the SQLite option it works perfectly.
I'm using two replicates (so for samples total) and a refseq gtf annotation file. I have also tried using both output from Cuffmerge and Cuffcompare as my input for Cuffdiff, but the result is the same.
Any ideas what is happening?
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modified 3 months ago
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Jennifer Hillman Jackson ♦ 25k
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3.2 years ago by
nevil • 20
Hello,
Would you be able to share a history with galaxy-bugs@lists.galaxyproject.org? We can confirm inputs and if this is a true bug, get it ticketed for a correction. Please include a link to this question in the comments and be sure that all inputs/outputs from the sample errors are left undeleted.
Thanks, Jen, Galaxy team
Hello,
I'm having an issue with cuffdiff output- everything's in tabular format. How do I manipulate to use it in cummerbund? Please help.
Thanks, Vaish
I am also having the similar problem as Vaisharaghu has posted.Please help as soon as possible.
I am also having this same problem. I've duplicated the run and when I run the data to generate SQLite for cummeRbund it errors but when I disable that function with all else the same, it works perfectly.
Hello nevil!
Questions similar to yours can already be found at:
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Cheers!