Bitwise Flag Samtools

Question

[rob234king]

If I have mapped reads to a reference and I want to extract unmapped reads of corresponding paired reads that did map, will this flag do it or would it pull out the aligned reads which have a mate that didn't map?

0x0008 U the mate is unmapped

Answer 1

[BruceB]

It will give you aligned reads whose mate did not map.

You want to use -f 5 -F 8

So this will include reads with both the following: 1 = Read paired 4 = Read unmapped

But exclude reads with: 8 = Mate unmapped (i.e. it will just include the reads whose mate has not mapped)

[rob234king]

Thanks seemed to have worked, used alternative two steps, didn't realise you could combine them. thanks again.