hello all. i am working on RNA seq analysis. i would like to know following things: first i downloaded genome fasta file for non-coding rna from ensembl and got the gtf file for hg38 from there itself. performed hist2 and got 17% alignment for my sample against ncrna genome. now i sorted the file and then ran feature counts with the hg38 gtf file. but got zero counts, where is the issue.
also i would like to know. my bam file after sorting has the SRR id at first whereas the GTF file has chromosome no: . can this be a issue?