Thanks for your help. I'm mapping reads from one organism to a related but
different organism, so some of the parameters I'd like to adjust are to relax
mapping stringency -specifically:
-n 3 (allow 3 mismatches in seed)
-e 250 (allow cummulative phred score of 250 [or some other value
Hi Metge,
Thank you for your kind comments!
The GATK tool wrappers are still in an early beta stage of development.
Because of this, we are not ready to support set-up in local instances yet.
If you have functionality input for the version on our Test server,
general feedback is welcomed on
A peculiar bug, presented for your input:
A colleague has built a few tools and is trying to incorporate them into
a workflow. However:
1. When he creates an new empty workflow, edits it and adds the
tools, they appear without inputs (i.e. the icons/boxes on the diagram
have no input
Hi Franzi,
You have one too many hg19 in there. The fields go like:
unique_build_id dbkey display_name fasta_file_path
valid_tool_suites
so:
hg19hg19hg19 /drive1/galaxy/reference/hg19/sam_index/hg19_ref.fa
gatk
But do note that these tool integrations are still
Clare
I wonder if you would be open to share the details of your setup and what you
had to do for this once you are done. I think it would be incredibly useful to
community (at least it would be for me ;-))
Thanks!
On Nov 17, 2011, at 5:14 PM, Clare Sloggett wrote:
Hi Enis, Jeremy,
On Fri, Nov 18, 2011 at 12:56 AM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
Scalability issues are more likely to arise on the back end than the front
end, so you'll want to ensure that you have enough compute nodes. BWA uses
four nodes by default--Enis, does the cloud config change this
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