pysam: Use read ID to access location

Question

[bd2810]

I know the read_ids of my reads, but I want to know, i.e. "chr1:100-120". Therefore I'm trying to access the read from a bam/sam file using the read id but I have not had any luck with pysam so far. Does anyone know how I could do this?

[Bastien Hervé]

It's always clearer with an example. Do you want to access the sequence of your read using chr1:100-120 or the possible gene at this position ?

Could you detailed this please :

I want to know the location

Answer 1

[Devon Ryan]

You can't do that, you can only iterate over all of the reads and check if they match your read_ids. Note that this is not a limitation of pysam, it's implicitly not meant to work in the BAM and CRAM formats.