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Old 12-13-2011, 04:56 AM   #5
marb
Junior Member
 
Location: Poland

Join Date: Dec 2011
Posts: 7
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I've tested cufflinks processing on other data and then cufflinks recognised them correctly as 57bp x 57bp.
Hence I know that there is the mistake at tophat processing fastq files level.

I know that is necessary to all sequences R1 and R2 (pair-end) be typed in the same order, so I used following command:

Code:
tophat /path/to/genome $(printf "%s," ./*.gz | sed 's/,$/\n/')
Do you think that way type args (fastq files) is incorect?
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