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Question: How do I add my own reference genome for mapping RNA-seq data
1
gravatar for gyan.sahukhal
14 months ago by
gyan.sahukhal • 10
gyan.sahukhal • 10 wrote:

How Do I Add my own reference genome for mapping RNAseq data?

Below is the link for the reference genome of my interest.

https://www.ncbi.nlm.nih.gov/nuccore/NC_007793.1
rna-seq reference genome custom • 716 views
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modified 14 months ago by Jennifer Hillman Jackson ♦ 25k • written 14 months ago by gyan.sahukhal • 10
1
gravatar for Jennifer Hillman Jackson
14 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If working at a Galaxy server that you do not administrate, use the genome as a Custom reference genome.

If working at your own Galaxy, the manual instructions 18Kbeyond give should work, but using Data Managers instead is recommended unless you are very familiar with line-command admin tasks within Galaxy.

  • Data Managers are installed from the Tool Shed like other tools (from the Admin panel)
  • Fetch the genome creating a dbkey
  • Index for Samtools, Picard, and TwoBit (2bit)
  • Index for downstream tools
  • The DMs are named similar to the data they index, see Category Data Managers at http://usegalaxy.org/toolshed to review

Thanks, Jen, Galaxy team
ADD COMMENT • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for 18Kbeyond
14 months ago by
18Kbeyond • 20
New York
18Kbeyond • 20 wrote:

First, index samples and save them in a path. say home/galaxy/galaxy_data/genomes/

Then, make changes like below in tool-data/bwa_mem_index.loc according to tool-data/bwa_mem_index.loc.sample

hg19bwa hg19 hg19 Canonical /home/galaxy/galaxy_data/genomes/hg19/bwa/hg19.fa

mm10bwa mm10 mm10 Canonical /home/galaxy/galaxy_data/genomes/mm10/bwa/mm10.fa
ADD COMMENT • link written 14 months ago by 18Kbeyond • 20
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