(1)Do those reads mapping to genome corrdinate with the SQ header in the accepted_hits.bam
(2)why do many FPKM=0 in the cufflinks result, the command line I used
cufflinks -p 6 -g gencode10.gtf -N -b hg19.fa -u --library-type f
r-firststrand -o cufflinks/$i tophat/accepted_hits.bam"
(2)why do many FPKM=0 in the cufflinks result, the command line I used
cufflinks -p 6 -g gencode10.gtf -N -b hg19.fa -u --library-type f
r-firststrand -o cufflinks/$i tophat/accepted_hits.bam"