I am trying to merge 3 .bam files (different alignments of the same ChIP-seq run), one has 5.9M reads, one 1.2M and one 0.4M. However after running merge bam files in sam tools I only get back a file with 4.2M reads in it (at least the output of rmdup tells me I have 4.2M reads). Any ideas as to why I seem to have lost 3M or so reads during merging of files?
Many thanks
Dave
Sorry, how do you merge with different read groups, there doesn't seem to be an option for that using merge bam files in SAM tools?
Oh that can be, please use the picard tools for that.
David,
Bjoern is correct - this is a two step process (at this time). First run the tool "NGS: Picard (beta) -> Add or Replace Groups" to add read groups to each of your BAM files. Second, run the tool "NGS: SAM Tools -> Merge BAM Files".
This may seem like a lot of steps (if you are also grooming, etc.), but you can put all (or most) of these operations into a workflow once you have a consistent process.
Thanks! Jen, Galaxy team
I don't think so
Hi David,
are the sinigle BAM files already rmdup'ed?
Yes, they had been.
Have you specified different read groups?