[SpreeFu]

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!

[nicrob]

I attempted to explain this here: http://seqanswers.com/forums/showthread.php?t=29621

Hi all,

According to the description of the output file genes.fpkm_tracking of cuffdiff, the value of *_FPKM is larger than *_conf_lo and smaller than *_conf_hi. But in my results, 12257 of 91991 transcripts in one sample have FPKM larger than both conf_lo and conf_hi. Is it normal?

The cufflinks version 2.1.1 was used.

[jordiabante]

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.

- Jordi