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
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rob234king
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)
Thanks seemed to have worked, used alternative two steps, didn't realise you could combine them. thanks again.
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