populating the pull-down menu: reference genomes (built-in index)
Hi, We are trying to put a few reference genomes into the built-in index for bwa, bowtie, bowtie2 and tophat. For the human hg19 we can find those. However, we also like to upload the Rhesus macaque genome and haven't been able to find an indexed version at NCBI or other places. Are other genomes pre-indexed for these applications somewhere? How do those files look like exactly (extensions, number of files needed, etc.)? How would we index the Rhesus genome for the above mappers if they are not available in an indexed form? Thank you, Jeannette CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
Hello Jeannette, Data is available from our rsync server, as explained here: http://wiki.galaxyproject.org/Admin/Data%20Integration See "Get the data" If you need to make indexes that we do not have, each tool's original documentation will have general instructions and the Galaxy .loc file has instructions for how to configure so that these are usable by tools. We also give specific instructions for many here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Hopefully this helps, Jen Galaxy team On 5/22/13 10:45 AM, Staheli, Jeannette wrote:
Hi,
We are trying to put a few reference genomes into the built-in index for bwa, bowtie, bowtie2 and tophat. For the human hg19 we can find those. However, we also like to upload the Rhesus macaque genome and haven't been able to find an indexed version at NCBI or other places.
Are other genomes pre-indexed for these applications somewhere?
How do those files look like exactly (extensions, number of files needed, etc.)?
How would we index the Rhesus genome for the above mappers if they are not available in an indexed form?
Thank you,
Jeannette
CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
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Jennifer Jackson -
Staheli, Jeannette