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Old 10-27-2014, 11:48 PM   #2
sdriscoll
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I think you have to run cufflinks one time per BAM file. That's how I have always done it and that's how it would handle things internally anyways since each set of alignments would be interpreted independently of the others. If you can supply multiple BAMs in a single command then I'd expect the program to pool them and evaluate them as a single sample.

--GTF is a mode for quantification only. --GTF-guide is a mode for quantification plus de-novo assembly of isoforms from alignments using a supplied GTF as a guide (like giving it a starting point for de-novo assembly). --GTF-guide uses a sligntly different assembly strategy than the default (without --GTF or --GTF-guide).
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/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
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