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Old 11-18-2015, 03:36 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,077
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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

Code:
/path_to/sample1_clout/transcripts.gtf
/path_to/sample2_clout/transcripts.gtf
/path_to/sample3_clout/transcripts.gtf
Replace "path_to" with real file paths on your system.
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