I want to map Leishmania major RNAseq raw reads from SRA to Leishmania major reference genome using RNA STAR. I use this tutorial. But galaxy doesn’t have a Leishmania major built in reference genome so I got the genome FASTA file and gff file of Leishmania major from TriTrypDB database. You can get access to these files from here.
When I run the RNA STAR, I get an error. What is wrong within what I do?
I enter these two files using “Upload Data” on galaxy and then click on Choose local files. I select the two files in my computer and then click on Start button. I don’t change the default selected items for Type, Genome, or Settings because I don’t know what to change.
Then I use RNA STAR with the following settigs and keep all other options without change:
Custom or built-in reference genome:
Use reference genome from history and create temporary index
Select a reference genome:
I select the FASTA file
Build index with or without known splice junctions annotation:
Build index with gene-model
Gene model (gff3,gtf) file for splice junctions:
I select the gff file
Then I click on the execute button