Hi Ross,
thanks for your answer. I found a dirty fix for merging pairs of bam files,
had to change a couple of things in my local installation though.
- Add group reads to each BAM file separately using Picard's Add or Replace
Groups http://localhost:8080/tool_runner?tool_id=picard_ARRG (with
Hello Tarek,
If you want to reduce the number of identical reads, then please see the
tool FASTA manipulation - Collapse sequences. Converting formats
would be necessary, the tool Tabular-to-FASTA can perform this operation.
Best,
Jen
Galaxy team
On 8/2/11 3:57 PM, tarek addwebi wrote:
IGV should allow you to do this but not sure about trackbrowser in Galaxy.
Vasu
--- On Wed, 8/3/11, Jiannong Xu j...@nmsu.edu wrote:
From: Jiannong Xu j...@nmsu.edu
Subject: [galaxy-user] visualization
To: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu
Date: Wednesday, August 3,
Hi, Camille,
I can see this really needs a 'proper' fix - preferably taking
advantage of the automated header merge.
Preserving the metadata from each bam automatically is safer and less
error-prone but you could use the existing Replace sam/bam header
tool to do the surgery once you have a
Hi, Camille.
If you can find some time to upload some of your bam files, could you
please test the revised bam merge tool on http://test.g2.bx.psu.edu/
and let me know how you go. This won't be on the main site until the
next scheduled update in a few weeks.
If you need this locally, the changes
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