RNA-seq analysis

Question

[sk_24]

I have paired-end FASTQ files. I used HISAT2 for alignment and got a good alignment percentage. Then, I used featurecounts for getting the raw counts for the genes. I excluded the chimeric fragments using -C command, but I see that most of my reads fall under unassigned chimera and very few are assigned. What could be the issue with it?

[rfran010]

More info would be useful, such as some example chimeric reads and some numbers to qualify "most" and "very few", but most reads being chimeric sounds strange.

Few reads being assigned may make sense depending how few and the library type.

For chimeric reads, that would be something that happens during alignment though, so would be good to investigate what are those reads.