Question: Insert Size For Each Bam Entry
0
gravatar for Nicolas Rosewick
4.2 years ago by
Belgium, Brussels
Nicolas Rosewick6.3k wrote:

Hi,

I've a bam file and I want to know the insert size for each entry. I know that picard CollectInsertSizeMetrics gives me statistics about insert size, but is it possible to have it for every entry ?

thanks

bam • 1.9k views
ADD COMMENTlink modified 4.2 years ago by Vitis1.6k • written 4.2 years ago by Nicolas Rosewick6.3k
1
gravatar for Ashutosh Pandey
4.2 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

The ninth column of the SAM file (TLEN) approximately represents the insert size. Subtract length of a read (For example 75 bp or 100 bp) from TLEN to get the insert size. See this earlier post from me:

estimating Insert size from paired end data.

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Ashutosh Pandey11k

I know I'm late. But, given the information at http://thegenomefactory.blogspot.de/2013/08/paired-end-read-confusion-library.html, are you sure about substracting?

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by seta970
0
gravatar for Vitis
4.2 years ago by
Vitis1.6k
New York
Vitis1.6k wrote:

Please see Bio::DB::Sam perl API for accessing SAM and BAM files. It has an explicit function to fetch the insert size for each mapped read pair. http://search.cpan.org/~lds/Bio-SamTools/lib/Bio/DB/Sam.pm#BAM_Files

ADD COMMENTlink written 4.2 years ago by Vitis1.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1137 users visited in the last hour