Question: HISAT2-reference genome not available in a local -- data must be installed first
gravatar for c2c12
10 days ago by
c2c120 wrote:

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.

ADD COMMENTlink modified 10 days ago by Jennifer Hillman Jackson25k • written 10 days ago by c2c120
gravatar for Jennifer Hillman Jackson
10 days ago by
United States
Jennifer Hillman Jackson25k wrote:


The hg19 genome is indexed for HISAT2 at Galaxy Main 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:

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.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 10 days ago by Jennifer Hillman Jackson25k
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