Dear Sir/Madam,
I am a registered user of the public Galaxy Server (main). I was trying to
upload two files (one is 1.6G and the other is 1.9G) but it was labeled as
Job is waiting to run forever. Could you please let me know the possible
reasons?
Sincerely,
Yan
Hi Mathew,
Regarding 1 you might want to read this thread:
http://user.list.galaxyproject.org/Problem-with-Depth-of-Coverage-on-BAM-files-GATK-tools-td4654147.html
All tools from GATK are limited to hg_g1k_v37 as far as I know.
Best,
Carlos
On Mon, Aug 6, 2012 at 10:30 AM, Mathew Bunj
Hello Yan,
Help for using a Custom reference genome is on this wiki and the links
it points to:
http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
Hopefully this helps,
Jen
Galaxy team
On 8/6/12 9:10 PM, Yan He wrote:
Hi everyone,
I am wondering if I can use user-defined reference
Hello Mathew,
Carlos is correct the the tools in the group NGS: GATK Tools (beta)
will require that the data is mapped/associated with the reference
genome hg_g1k_v37. Belinda has offered to help with the details that
go beyond Galaxy and that is great - the GATK forum is definitely the
best
Hello IB,
Instructions for loading, formatting, troubleshooting fasta datasets is
including in this wiki and the links it points to:
http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
As for the source, NBCI would be the first choice. We cannot really
vouch for other sites but
Hi Kanwar,
I found that you also posted this question and another like to the
Google group for SICER on 7/10 and received some help there:
http://groups.google.com/group/sicer-users
Glad that you were able to get the questions resolved. For others
reading this post or interested in SICER
Hello Mathew,
The short answer is yes, Galaxy has many tools to do this type of analysis.
If you are new to Galaxy, you will probably want to start in these
places to get acquainted with the UI and tool organization:
https://main.g2.bx.psu.edu/u/james/p/exercises
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