I'm processing 2 RNA-seq data. One has a fragment insertion size less than 30 bp, the other less than 500 bp. The mapping result from STAR is good, both of them have more than 95% reads with a MAPQ value > 10. However, what made me confuse is that, when I used featureCounts to count the reads to mouse mm10 GTF file, gencode.vM15.annotation.gtf. Only a small amount of reads can be successfully assigned. The 30 bp library had a assigned rate of only 27%, and the 500bp has a rate of 29%. So many reads were lost! I don't know if it is normal. Or, I have done something wrong? My command line is like this,
featureCounts -T 20 -t exon -g gene_name -a gencode.vM15.annotation.gtf -o counts.txt sample.bam
Could anyone give some suggestions? Thank you so much.