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?