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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