Extract reads based on the orientation of the mapped reads.

Question

[kaz0816]

I want to extract reads from a BAM file based on the orientation of the mapped reads. I want to extract the reads of each category separately based on the orientation of the reads such as LR (Illumina pair-end reads), RL (Illumina mate-pair reads), RR or LL as depicted in IGV. Please tell me if there is any solution to that.

Answer 1

[colindaven]

You can use bamtools for this. Look at the tutorial PDF here:

https://github.com/pezmaster31/bamtools/wiki/Using-the-toolkit

You have to write a config file for it.

[kaz0816]

I understand that the "bamtools split" command retrieves those reads. However, I still don't know the FLAG setting when dividing into pair-end reads (LR:-> <-), mate pair (RL: <- ->) and others (RR or LL).
I would appreciate it if you could explain it in an easy-to-understand manner.