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samtools view -l/-r options
Hi everyone!
Is it possible to retrieve mapping results of several specific reads from bam or sam files by referring to the read names?
I tested the following options and couldn't get it working:
-l STR only output reads in library STR [null]
-r STR only output reads in read group STR [null]
-R FILE list of read groups to be outputted [null]
I have a txt file that includes names of several candidate reads, and I would like to extract the mapping info of the reads from a bam/sam file.
Could some one please provide an example script on how to do that?
Thank you!
Cheers.
Is it possible to retrieve mapping results of several specific reads from bam or sam files by referring to the read names?
I tested the following options and couldn't get it working:
-l STR only output reads in library STR [null]
-r STR only output reads in read group STR [null]
-R FILE list of read groups to be outputted [null]
I have a txt file that includes names of several candidate reads, and I would like to extract the mapping info of the reads from a bam/sam file.
Could some one please provide an example script on how to do that?
Thank you!
Cheers.
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