I was trying to use Galaxy’s RNA-STAR and HISAT2 tools to create read count files for my RNA sequencing data, but there is no zebrafish (Danio rerio) reference genome available. I’m interested in the zebrafish genome and gene model, and it’s not available in either the RNA-STAR or HISAT2 tools. Any suggestions for troubleshooting this?
The genome I need is from a zebrafish (Danio rerio).
Thanks
Hi @lterrazass
You’ve right: I checked Galaxy Australia and HiSAT2 does not have the D. rerio assembly.
Go to the Downloads section at the UCSC Genome Browser site, select Genome Data, find the latest zebrafish genome assembly and upload the genome assembly (gzipped fasta) and gene annotation (I have less issues with GTF) to Galaxy of your choice. Use upload by URL: copy link to a file at UCSC and paste the URL into Galaxy upload menu, Get/Fetch data section.
During HiSAT2 job setup change Source of genome to In History. HiSAT2 will index the genome and map reads.
Hope that helps.
Kind regards,
Igor
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Thank you very much!