[Bioperl-l] fetching all alignments from a sam/bam by read header in perl

Abhishek Pratap abhishek.vit at gmail.com
Fri Feb 24 09:58:33 EST 2012


Hi Peter

You got it right.

Here is the link :
http://biostar.stackexchange.com/questions/17787/fetching-all-alignments-from-a-sam-bam-by-read-header-in-perl



-A

On Fri, Feb 24, 2012 at 1:24 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Fri, Feb 24, 2012 at 12:55 AM, Abhishek Pratap
> <abhishek.vit at gmail.com> wrote:
>> I am wondering if there is a slick way access all the possible
>> alignments for a read present in sam or bam file given the read
>> header. Since the existing codebase is in perl I would prefer
>> something which can be done in/via perl.
>>
>> By default BAM's are indexed by location so the inbuilt samtools
>> indexing wont work I guess.
>>
>> I should also say the input bam file will have in the order of 500
>> million total alignments and many reads are expected to be aligned to
>> more than one place in the genome. Given the size of the data loading
>> it all in one big hash is not turning out to be memory friendly.
>
> Are you asking for SAM/BAM read lookup by read name?
>
>> PS:  I also posted this earlier on Biostar.
>
> Link?
>
> Peter



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