Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Customizing Mm9 Mouse Reference Genome And Then Using That As The Ref Genome When Uploading Illumina Data
0
gravatar for Christopher Callaway
7.1 years ago by
Christopher Callaway • 40
Christopher Callaway • 40 wrote:
I would like to filter out the mm9 mouse build ref genome to only show MspI sites, and then use that as my "Genome" when uploading my Illumina data. Anyone have a protocol for that? Thanks, Christopher W. Callaway University of Utah Dept. of Pediatrics Division of Neonatology 417 Wakara Way #2222 Salt Lake City, UT 84108
• 1.1k views
ADD COMMENT • link •
modified 7.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.1 years ago by Christopher Callaway • 40
0
gravatar for Jennifer Hillman Jackson
7.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hi Christopher, The target "reference genome" can be any fasta file in your history, for most tools, including mapping tools. However, the assigned "database" attribute for any datasets that you want to map to this custom reference would be left as undefined in Galaxy (but this would have no impact on analysis). The exception here is if you were running your own instance. For this case, a native "reference genome" of the modified mm9 genome data could be loaded. As part of this process, you would be creating the database attribute "label", all of the indexes, and be able to assign the database attribute for datasets to this new database label. Instructions for local installs are in the wiki here: http://getgalaxy.org To get you started with the filtering, I can let you know that the mm9 database in Galaxy was sourced from UCSC http://genome.ucsc.edu and can be obtained from their Downloads site. Hopefully this helps, Thanks, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENT • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 175 users visited in the last hour