Dear Galaxy development team,

I am trying to analyze RNAseq data using the following pipeline:

I am able to run everything without a problem up to the CuffDiff step. I always get an error message. I sent a bug report and posted on Biostars-Galaxy. Jen replied to my comment on Biostars and recommended I email galaxy-dev.

Please see the details of the error message here: https://biostar.usegalaxy.org/p/18331/

I think it may have a problem loading the SQlite database? Even though CuffDiff gives an error message, I was still able to download the data from CuffDiff in tabular format and perform some data analysis using R. However, it would be useful to be able to use cummeRbund to analyze the cuffdiff data.

Thank you in advance for all your help. Let me know if there is any other information I can provide to clarify the error, etc.

Best Regards,

Ravi