Question: cummeRbund SQLite database error from Galaxy main CuffDiff tool
gravatar for nevil
2.6 years ago by
United States
nevil10 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?

rna-seq cufflinks galaxy R • 1.3k views
ADD COMMENTlink modified 2.6 years ago by Jennifer Hillman Jackson24k • written 2.6 years ago by nevil10
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson24k wrote:


Would you be able to share a history with 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

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson24k


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

ADD REPLYlink written 18 months ago by vaisharaghu0
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