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Old 11-18-2015, 04:36 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,132

Cuffmerge is not going to combine your bam files but it is going to merge several Cufflinks assemblies (gtf files) to give you a common representation.

Assemblies.txt is a simple text file (that you can make using an editor) where you specify paths to gtf files from each of the tophat runs, one sample per line. Like this

Replace "path_to" with real file paths on your system.
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