I have a SAM/BAM file and I'd like to grep for alignments of certain reads IDs.
I have the read ID strings in another file. I'm currently doing this with:
$ samtools view in.bam | fgrep -w -f read.ids > alignments.txt
Is it possible to parallelise the grep by having each grep process a different
On Fri, Aug 9, 2013 at 7:53 AM, Nathan S. Watson-Haigh
wrote:
>
> I have a SAM/BAM file and I’d like to grep for alignments of certain reads
> IDs. I have the read ID strings in another file. I’m currently doing this
> with:
>
> $ samtools view in.bam | fgrep -w -f read.ids > alignments.txt
It wi
Assuming your shell is bash
With this exported function
function slice {
# PURPOSE: After an optional -h lines of header (which are echoed
# unless supressed with <-sh>), echo every <-n>th line (default:
# every 1 line) starting with the <-m>th (counting from 1, starting
# with the first line
