Request --Index Arabidopsis thaliana TAIR 10 for HISAT2/Usegalaxy.org, Solution -- Use a Custom Genome or Usegalaxy.eu

usegalaxy.org support
1

Hello,

Would it be possible for you to add the Arabidopsis thaliana TAIR 10 genome to the list of built-in references for HISAT2?

Thanks,
Matt

1 Like
2

Hey Matt,

Why do you want to add the genome to the built in genome?

1 Like
3

Hi,

Some consolidation of reference genome, reference annotation, and associated indexes will be done between the usegalaxy.* servers, likely sometime this year.

  • TAIR10 is already on the list to be indexed for HISAT2 at Galaxy Main https://usegalaxy.org.* The version already available/indexed for some tools is from UCSC, so that is where you should also get the fasta for the genome if you decided to use the Custom Genome functions. Annotation would be best if sourced from iGenomes.

  • TAIR10 is already indexed for HISAT2 at Galaxy EU https://usegalaxy.eu.* This is also the UCSC version. iGenomes is still the best annotation source.

Custom Genome FAQ plus how to avoid chromosome mismatches when incorporating reference annotation (will probably be needed at either server).

Related Q&A that explains more about how to get iGenome annotation into Galaxy and avoid any content-level mismatch problems: What exactly are the "built-in references" in Galaxy's HISAT2?

Thanks!