I have feature counts with zero for most of genes in most of the samples. I am worrying as Alignment statistics shows 90% (12M reads aligned) so if not exon then where it is going and aligning.
Not all counts are zero, but for some specific genes i would expect counts to be higher in samples Following command i have used
featureCounts -p -t exon -g gene_id -a Refseq.gtf -o output.txt sample.bam -M -O
For Example this is feature count of CXCL2 gene in different samples
CXCL2 1 0 0 0 0 0 0 0