Hi all, is it possible to count the reads mapping to a specific region of a gene from the accepted_hit.bam?
Thanks a lot!
Thanks a lot!
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I attempted to explain this here: http://seqanswers.com/forums/showthread.php?t=29621
Originally posted by pengchy View PostComment
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Hi Cole,
I tried to reproduce the results in the paper "Differential gene and transcript expression analaysis of RNA-seq experiments with TopHat and Cufflinks" but using TopHat2 and Cufflinks2 instead. According to the volcano plot generated by cummeRbund (built on R 3.2.2) there are no significant differences. However, there're a bunch of genes above -log10(p-value)=2 and distant from log2(fold change)=0 in it.
Please, I would really appreciate if you could give me some feedback on this.
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