Question: Bitwise Flag Samtools
1
gravatar for rob234king
5.5 years ago by
rob234king570
UK/Harpenden/Rothamsted Research
rob234king570 wrote:

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

samtools • 1.8k views
ADD COMMENTlink modified 5.5 years ago by BruceB330 • written 5.5 years ago by rob234king570
1
gravatar for BruceB
5.5 years ago by
BruceB330
Cambridge, UK
BruceB330 wrote:

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)

ADD COMMENTlink written 5.5 years ago by BruceB330
1

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

ADD REPLYlink written 5.5 years ago by rob234king570
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