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Old 08-22-2011, 05:57 PM   #1
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Location: South Korea

Join Date: Aug 2011
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Default first read in a pair means F3 or R3?

I am trying to extract unmapped reads afte resequencing SOLiD mate-pair reads.
This is what I know so far..

The command "samtools view -f 0x0048", gives me a list of reads whose pairs are unmapped and the reads are the first read in a pair.

The command "samtools view -f 0x0088", gives me a list of reads whose pairs are unmapped and the reads are the second read in a pair.

I have an idea that I can get a list of unmapped reads using these commands somhow.
What I don't understand is what exactly the "first" or "second" read in a pair means.
Does the "first" read in a pair represents F3 or R3?

It would be really helpful if someone can clarify this.

Thank you very much!

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Old 08-24-2011, 10:10 AM   #2
Nils Homer
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Posts: 1,285

First or second is annotated by the aligner, so can you tell us which one you used?
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