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
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
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