Question: Salmon: no built-in index reference transcriptome available
gravatar for matthew.johnson
16 months ago by
matthew.johnson30 wrote:

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...


rna-seq galaxy • 1.3k views
ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson25k • written 16 months ago by matthew.johnson30
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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): >

Thanks, Jen, Galaxy team

ADD COMMENTlink written 16 months ago by Jennifer Hillman Jackson25k

Thanks Jen.

For others: I downloaded the mouse cDNA fasta file here:

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

Running now...

ADD REPLYlink written 16 months ago by matthew.johnson30
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