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Old 11-22-2010, 08:53 AM   #1
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Location: USA

Join Date: Aug 2010
Posts: 103
Question cuffdiff0.9.2: output problem when input multiple SAM files

Hi all,
I wonder if any of you have run cuffdiff to compare >=3 samples. I did this with cuffdiff 0.9.2, the latest version. The command is:
./cuffdiff -p 10 -o <output dir> [reference gtf] sample1.sam sample2.sam sample3. sam
However, I did not get the *.diff files (i.e., 0_1*.diff) though I did get files such as gene_exp.diff, genes.fpkm_tracking etc.

Did I miss something?
Thank you all and happy thanks giving! :-)
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