I am working on RNA seq analysis and I would like to know the following things:
- downloaded genome fasta file for non-coding rna from ensembl and got the gtf file for hg38
- performed hist2 and got 17% alignment for my sample against ncrna genome
- sorted the file and then ran feature counts with the hg38 gtf file but got zero counts
- what could be the issue that is causing zero counts?
My bam file after sorting has the SRR ID at first whereas the GTF file has chromosome no: . Could this be the issue?