Count right and left mate pairs from Sam files

Question

[PAn]

Hello,

I have two separate left and right mate sam files from a sample's RNAseq data (these are unmapped sam files after running alignment both right and left mate fastq files) and I need to find out which of these reads come from pairs and which of these reads are left unmapped from either just left or right mate. ie. In the end I should be able to calculate this

1- % Reads common in left and right mate sam files
2- %Reads only in left mate sam file
3- %Reads only in right mate sam file

can someone please suggest on how to do it? Should I read the read names in hash and compare the ids?

Thanks!

Answer 1

[Brian Bushnell]

You should really map the reads paired, which will (typically) only generate a single sam file containing both mapped and unmapped reads. It's not clear to me how you ended up where you are, or what you're trying to do, but mapping is much more accurate when reads are paired.

Answer 2

[abascalfederico]

I think samtools flagstat will give you that

[PAn]

flagstat would run on each sam file separately and i think will not compare based on read names between two files. I am trying to write a script to do this now.