Hi Jen,

Thanks for the information. I used this setting and the merged BAM files 
(.accepted hits) worked quite well for the downstream analysis.

Best,

Jianguang

________________________________
From: Jennifer Jackson [j...@bx.psu.edu]
Sent: Tuesday, April 09, 2013 4:10 PM
To: Du, Jianguang
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Parameters for merging BAM files

Hello Jianguang,

This setting is recommended to be used. It will merge all headers, but if there 
are differences between the input files these will be combined together in the 
final output.  If you want to see what this content will be, convert the BAM 
files before and after the merge to SAM format (using the option to include 
headers) and review the results. You can always later delete these permanently 
to recover disk space.

Hopefully this helps,

Jen
Galaxy team

On 4/5/13 1:22 PM, Du, Jianguang wrote:

Hi All,

I want to merge the Tophat output (Accepted Hits) of Several datasets. I want 
the merged BAM file has the exact format as the individual input BAM files, 
should I check "Merge all component bam file headers into the merged bam file"?

Thanks.

Have a nice weekend.

Jianguang



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___________________________________________________________
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