Samtool: Combine Bam Files With Different Tag Sizes

Question

[Lisanne]

Dear All,

I want to compare 2 chip-seq data files (BAM files) into one file. The problem is that 1 chip-seq has a tag size of 50 and the second chip-seq has a tag size of 100. Is there a way to merge them? Is the different tag size length a problem?

THanks!

Lisanne

Answer 1

[Damian Kao]

You can use [?]Samtools[?] (http://samtools.sourceforge.net/) or [?]Picard tools[?] (http://picard.sourceforge.net/command-line-overview.shtml) to merge your bam files into one single bam. There should be no problem in merging two bam files of differing read lengths.

Answer 2

[Chris Miller]

Assuming the bams are already sorted. it's as easy as:

samtools merge combined.bam 1.bam 2.bam

The read lengths don't matter from the perspective of a bam file. They might, however, matter to some of the algorithms you wish to apply. You should be aware of that possibility.