Tool: Merge Bam files
0
gravatar for david.fear
3.3 years ago by
david.fear10
European Union
david.fear10 wrote:

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

tool samtools • 3.6k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by david.fear10

Hi David,

are the sinigle BAM files already rmdup'ed?

ADD REPLYlink written 3.3 years ago by Bjoern Gruening4.7k

Yes, they had been.

 

ADD REPLYlink written 3.3 years ago by david.fear10
1

Have you specified different read groups?

ADD REPLYlink written 3.3 years ago by Bjoern Gruening4.7k
1
gravatar for david.fear
3.3 years ago by
david.fear10
European Union
david.fear10 wrote:

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?

 

ADD COMMENTlink written 3.3 years ago by david.fear10

Oh that can be, please use the picard tools for that.

ADD REPLYlink written 3.3 years ago by Bjoern Gruening4.7k
1

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

ADD REPLYlink written 3.3 years ago by Jennifer Hillman Jackson22k
0
gravatar for david.fear
3.3 years ago by
david.fear10
European Union
david.fear10 wrote:

I don't think so

ADD COMMENTlink written 3.3 years ago by david.fear10
1

Please try to merge them with different read groups that should be what you want, I assume.

ADD REPLYlink written 3.3 years ago by Bjoern Gruening4.7k
0
gravatar for david.fear
3.3 years ago by
david.fear10
European Union
david.fear10 wrote:

Thanks. I'll give it a go.

 

ADD COMMENTlink written 3.3 years ago by david.fear10
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