How extract read ID from a bam file per mapped feature (gene)

Question

[valopes]

Hi everybody,

I have a bam file, from a mapping done with minimap2, and I need to extract the read IDs based on the genome features (gff3). Let's say: read A was mapped on the features (genes) 1 and 2 (if multiple mapped); read B was mapped on the feature (gene) 3

Actually, I am trying to figure out the best way to extract more info from Liftoff analysis, where outputs do not clearly show the correlation between features.

Does anyone have any ideas?

Thank you in advance!

[GenoMax]

Looks like you are looking for secondary alignments. You could look at the SA tags in the alignments.

[valopes]

It is not secondary alignments.

I want to know which read (read ID) mapped in a determined gene. So, it would be something like

• read 1 - gene B
• read 2 - gene A ....so on

[GenoMax]

It may be best to do this the other way. Get a BED file with gene co-ordinate intervals from a GTF file. Find out which reads are aligned to those intervals using samtools view region.

[valopes]

Thank you! I will try it and let you know how it goes...