Hi Laurent,
There's no command in samtools for that. You could write a small program to
do that relatively easily with pysam or something similar (or the samtools
C API, if you prefer). Alternatively, a bit of scripting and either
bedtools or bedops would work.
Devon
--
Devon Ryan, Ph.D.
Email: [email protected]
Laboratory for Molecular and Cellular Cognition
German Centre for Neurodegenerative Diseases (DZNE)
Ludwig-Erhard-Allee 2
53175 Bonn
Germany
<[email protected]>
On Wed, Jun 4, 2014 at 4:58 PM, Laurent MANCHON <[email protected]>
wrote:
> -hi,
>
> i want to know how many reads map 2 regions separated by a gap.
> Is there a command to report the count of reads that overlap 2 distincts
> region on the same sequence, i.e: chr1 4913-4963 & chr1 5390 5464
>
> thank you --
>
>
>
>
>
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