I'm having quite abit of trouble handling my RNAseq fastq files. These were originally obtained from a single cell RNAseq experiment (probably not relevant). As usual I map back to mm10 using HISAT2 and then using a UCSC GTF I check for hits using htseq. The issue is that htseq doesn't seem to pick up any hits, it only does so in 1 or 2 genes.
I thought something might be wrong with my aligning so loaded the bam. file from hisat into IGV just to check where the reads fall and they do fall in genes, definitely more than 2 so im not sure what I'm doing wrong with my htseq settings. Any suggestions?