The most strange thing happened. I aligned a sample of raw RNA-seq data with HISAT2 (default settings). Then I used the function [Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region] to cut a 20 kb region that I am interested in. I don’t have a lot of storage space. So far so good. But when I opened it in IGV, there were more than 20 kb, way more. I could see the entire chromosome. I checked two more chromosomes and they were empty.
This happened with only one sample but I have 9 from the same batch that are processing right now.
I have followed this protocol before and nothing like this happened. The only time when I could see more outside my region, it was solely because the ends of the exon were exceeding it. Which made sense.
Do you have any opinions about it?
BTW I checked and the region that I selected was the right one.