first read in a pair means F3 or R3?

yhong · 08-22-2011, 05:57 PM

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!

Best,
yhong

nilshomer · 08-24-2011, 10:10 AM

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

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08-22-2011, 05:57 PM	#1
yhong Junior Member Location: South Korea Join Date: Aug 2011 Posts: 3	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! Best, yhong

08-24-2011, 10:10 AM	#2
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	First or second is annotated by the aligner, so can you tell us which one you used?