Usually, I can get FPKM from cuffdiff & cufflinks.
If I have a only one sample, how can I get the FPKM value?
Cufflinks, rsem, kallisto, etc.
I tried cufflinks -M hg19.gtf --library-type fr-firststrand -o cufflinks_out tophat_out/A_accepted.hits.bam
Then, message was
[09:29:59] Loading reference annotation'
[09:30:01] Inspecting reads and determining fragment length distribution
>Processing Locus gi|387825349 [ ]0%
Is that right? I waiting for 3hours.. but nothing happend
Cufflinks isn't known for being fast. You might instead try cuffquant.