To perform bias correction using sequence data in
Cufflinks/Cuffcompare/Cuffdiff, you'll need to set up and add entries to
sam_fa_indices.loc
Of course, this isn't the most intuitive place, and we're planning to improve
loc file structure and usage in the future.
Best,
J.
On Mar 1, 2013, at
I have a local install of Galaxy. Tophat2 and Cufflinks work. cuffcompare
and cuffmerge do not. Errors are below.
There isn't a .loc file for cufflinks (overall). It will run if I don't
'use sequence'. It appears that the name of the database (dbkey) is
inherited from the Tophat2 output file,
