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Hello,
I used Cuffdiff 2.1.1 to analyse and compare 3 different experimental conditions, all together. I followed the command mentionned in the manual : cuffdiff <options> condition1_replicate1,condition1_replicate2,condition1_replicate3 condition2_replicate1,condition2_replicate2,condition2_replicate3 condition3_replicate1,condition3_replicate2,condition3_replicate3
The replicates were provided in comma separated list and conditions were provided with space separated list (as requested).
The results showed only the comparisons for condition 1 and 2. I also tried to analysed as time serie with -T option but without success.
Do I have to use another specific option ? is there a bug reported for this version of Cuffdiff ?
Thanks for your comments.
Benoit
I used Cuffdiff 2.1.1 to analyse and compare 3 different experimental conditions, all together. I followed the command mentionned in the manual : cuffdiff <options> condition1_replicate1,condition1_replicate2,condition1_replicate3 condition2_replicate1,condition2_replicate2,condition2_replicate3 condition3_replicate1,condition3_replicate2,condition3_replicate3
The replicates were provided in comma separated list and conditions were provided with space separated list (as requested).
The results showed only the comparisons for condition 1 and 2. I also tried to analysed as time serie with -T option but without success.
Do I have to use another specific option ? is there a bug reported for this version of Cuffdiff ?
Thanks for your comments.
Benoit