Hi,
i know this will be sticky question.. but i didnt find the answer..
i am using CuffDiff for DE between 2 condition.
i have 3 replicates for each.
The size of the number of reads that i have for each sample is variable..
3M,10M,20M,0.7M and so on..
when i used CuffDiff as:
cufflinks-1.3.0.Linux_x86_64/cuffdiff -N -o cuffdiff/2v10 cuffmerge/al/merged.gtf Tophat/case1/Trinity/Sample1/accepted_hits.sam,Tophat/case1/Trinity/Sample4/accepted_hits.sam,Tophat/case1/Trinity/Sample7/accepted_hits.sam Tophat/case1/Trinity/Sample2/accepted_hits.sam,Tophat/case1/Trinity/Sample5/accepted_hits.sam,Tophat/case1/Trinity/Sample8/accepted_hits.sam
i am getting 8000 genes in the list of DE.
it is not an usable number..
How can i reduce it?(Multiple Test as Bonferrony? BH?)
Thanks,
Pap
i know this will be sticky question.. but i didnt find the answer..
i am using CuffDiff for DE between 2 condition.
i have 3 replicates for each.
The size of the number of reads that i have for each sample is variable..
3M,10M,20M,0.7M and so on..
when i used CuffDiff as:
cufflinks-1.3.0.Linux_x86_64/cuffdiff -N -o cuffdiff/2v10 cuffmerge/al/merged.gtf Tophat/case1/Trinity/Sample1/accepted_hits.sam,Tophat/case1/Trinity/Sample4/accepted_hits.sam,Tophat/case1/Trinity/Sample7/accepted_hits.sam Tophat/case1/Trinity/Sample2/accepted_hits.sam,Tophat/case1/Trinity/Sample5/accepted_hits.sam,Tophat/case1/Trinity/Sample8/accepted_hits.sam
i am getting 8000 genes in the list of DE.
it is not an usable number..
How can i reduce it?(Multiple Test as Bonferrony? BH?)
Thanks,
Pap
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