Hi everyone, When I'm trying to use in my local galaxy HISAT2 for mapping the reads I have an information that reference genome is not available. I'm interested in grch37. I already downloaded one from Ensembl but I'd like to figure out how to use the one built in HISAT2. I'd be grateful for help with this issue. Z.
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Question: HISAT2-reference genome not available in a local -- data must be installed first
6 months ago by
c2c12 • 10
c2c12 • 10 wrote:
ADD COMMENT • link •modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 6 months ago by c2c12 • 10
6 months ago by
Jennifer Hillman Jackson ♦ 25k
Jennifer Hillman Jackson ♦ 25k wrote:
hg19 genome is indexed for HISAT2 at Galaxy Main https://usegalaxy.org. This is the UCSC version of GRCh37.
When using a local, you need to install the genome and indexes for tools. Genome data is not included in the distribution.
Best options -- all require that you are an administrator:
- Using Data Managers. https://galaxyproject.org/admin/tools/data-managers/
- Using Ephemeris. https://ephemeris.readthedocs.io/en/latest/
- Using CVMFS. https://galaxyproject.org/admin/reference-data-repo/
The final option is to use the genome as a custom reference genome. This uses much more resource than pre-computed indexes and you might run into memory problems, it depends on your configuration. It works well for small genomes (at any server) but even Galaxy Main can produce memory-related tool failures when using very large custom genomes like Human. https://galaxyproject.org/learn/custom-genomes/
Thanks, Jen, Galaxy team
ADD COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k
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