I have aligned my data ( paired end RNA-SEQ ) to genome ( Hg 19 - ensemble ) using tophat2 and with a GTF file and default options. When I give the same referance GTF file and
cufflinks ( v2.1.1 ), the
isoform.fpkm_tracking file has FPKM values of range
1.66072e-316 for some of the transcripts. Is it normal ? Can we consider them as less abundant transcripts and move on with downstream analysis ?
cufflinks command is
cufflinks -o outdir -p 5 -G ref.gtf sample.bam