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Old 07-08-2014, 07:49 AM   #1
Location: Istanbul, Turkey

Join Date: Oct 2012
Posts: 28
Default cuffcmp.combined.gtf vs. genes.gtf in CuffDiff

Hello all,

When I run CuffDiff with genes.gtf (annotation file I also used in Tophat2 when doing Transcriptome mapping) or cuffcmp.combined.gtf (generated by, cuffcompare -s /path/to/genome_seqs.fa -CG -r genes.gtf genes.gtf), I find different number of significantly differentially expressed genes. Is it normal? If it is which one is more suitable (I am only interested in genes_exp.diff at the output)?
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