c********e
发帖数: 598 | 1 I need to mask or filter "mapped reads" in sam/bam files using some
annotated tracks to generated new sam/bam files. How can I do it?
Please help! |
m******c
发帖数: 830 | 2 Don't know what you talking about. So can't help. |
n*********4
发帖数: 99 | |
u*********1
发帖数: 2518 | 4 samtools view -F 4 map.bam
4 (in decimal) or 0x0004 (in HEX) indicates that the query read is unmapped.
If you use the filter option (-F 4) you will remove unmapped reads, hence
the output will only contain mapped reads.
This flag will extract any mapped reads regardless of what mate pair looks
like.
If you'd like to account mate pair, please look at the link below:
http://www.biostars.org/p/14518/
【在 c********e 的大作中提到】
: I need to mask or filter "mapped reads" in sam/bam files using some
: annotated tracks to generated new sam/bam files. How can I do it?
: Please help!
|
c********e
发帖数: 598 | 5
unmapped.
Thanks for the reply. I already have mapped the read, I need further enrich
the reads using my own rules contain genomic region that I am interested.
【在 u*********1 的大作中提到】
: samtools view -F 4 map.bam
: 4 (in decimal) or 0x0004 (in HEX) indicates that the query read is unmapped.
: If you use the filter option (-F 4) you will remove unmapped reads, hence
: the output will only contain mapped reads.
: This flag will extract any mapped reads regardless of what mate pair looks
: like.
: If you'd like to account mate pair, please look at the link below:
: http://www.biostars.org/p/14518/
|
