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.
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