Salmon: no built-in index reference transcriptome available

Question: Salmon: no built-in index reference transcriptome available

16 months ago by

I'm trying Salmon for the first time and when I select "Use a built-in index" for the reference transcriptome it says "No options available." Perhaps these haven't been loaded/indexed for salmon yet?

Alternatively, what's the easiest way to import the right fasta format to my history, e.g., from UCSC or Biomart? The UCSC table browser has a Fasta export option but it's for multi-species alignments...

Thanks!!

rna-seq galaxy • 1.3k views

ADD COMMENT • link •

modified 16 months ago by Jennifer Hillman Jackson ♦ 25k • written 16 months ago by matthew.johnson • 30

16 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This tool will not have built-in indexes created. Instead, use a custom reference transcriptome.

Importing from the UCSC Table browser can sometimes result in truncated data. It is better to obtain the data from the Downloads area of the UCSC site in many cases.

Wherever the data is sourced, it can be formatted within Galaxy using the tool NormalizeFasta.

Custom genome help (same applies for custom transcriptomes): https://galaxyproject.org/support/ > https://galaxyproject.org/learn/custom-genomes/

Thanks, Jen, Galaxy team

ADD COMMENT • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen.

For others: I downloaded the mouse cDNA fasta file here: ftp://ftp.ensembl.org/pub/release-89/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz

I uploaded to Galaxy, ran it through the NormalizeFasta tool, and used it as the reference transcriptome for Salmon.

Running now...

ADD REPLY • link written 16 months ago by matthew.johnson • 30

Similar posts • Search »