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"?
Have a nice weekend.
This setting is recommended to be used. It will merge all headers, but
if there are differences between the input files these will be
together in the final output. If you want to see what this content
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,
Galaxy Support and Training