Using samtools to read a bam file
I am trying to extract some information (please see below) from a bam file using samtools. Given my lack of experience, I am struggling.
1.) Total reads aligned on the forward strand
2.) Total reads aligned on the reverse strand
3.) Number of read pairs where the pairs are pointing towards each other
4.) Number of read pairs where the pairs pointing in the same direction (this is the opposite of proper pairs)
5.) Number of primary alignments (not SECONDARY) that are on the forward strand
Any help would be greatly appreciated.
• 59 views
Read more here: Source link