Mapping Leishmania transcript using RNA STAR

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

Hi @Maryam_Momeni

This FAQ is focused on differential expression tools but it summarizes help for getting reference data organized, which applies for your use case too when running STAR.

Please give that a review, make data adjustments: minor format standardization resolves many errors across tools.

Then let us know if you need more help. This is how to share your input/parameter configuration and error:

:mechanic: What information should I include when reporting a problem?

Any persistent problems can be reported in a new question for community help. Be sure to provide enough context so others can review the situation exactly and quickly offer advice.

Consider Sharing your History or posting content from the Job Information :information_source: view as described in Troubleshooting errors.