Hello,
I have a list of genes and a list of RNAs. For each gene, I would like to know how many RNAs do not align. I am using hisat2 for alignments, and it gives me a fastaqsanger file with the unaligned reads, but the bam file always contains aligned reads.
Is there a way to obtain a bam file with counts for the unaligned reads? Alternatively, can I count how many unaligned reads there are for each gene from the fastaqsanger file?
I’m not sure I understand your question. An unaligned read is a read that has not been placed on the reference.
What exactly are you using as that reference, i.e. what are your exact inputs to hisat2?