Parameters for merging BAM files
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
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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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 [jen@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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
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Du, Jianguang -
Jennifer Jackson