Transcriptome input for Sailfish tool

Question: Transcriptome input for Sailfish tool

2.2 years ago by

Hi there,

I would like to run the sailfish tool, but I can't find a reference transcriptome to map the reads and the sailfish tool doesn't have any built-in reference transcriptome. Would it be possible to add it? (human transcriptome) or else, where can I get it from to import it into my library? Thank you in advance.

Andres

rna-seq reference sailfish input transcriptome • 1.1k views

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modified 21 months ago by csm165 • 0 • written 2.2 years ago by andres.caballero • 0

2.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There are no plans to include built-in reference transcriptome datasets at this time as these change and updated very quickly from the different data sources. Also, pairing between the reference transcriptome and the "File containing a mapping of transcripts to genes" inputs is critical for proper results.

Instead, obtain a set of reference mRNA reads (your "transcriptome") and the corresponding reference annotation (GTF or tabular format) from the same source at the same time. This ensures all the data will match correctly.

The RefSeq Genes track from UCSC http://genome.ucsc.edu is one choice.

hg hg38, the RefSeq bed file refFlat.txt.gz is here: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/
For hg38, the RefSeq transcript fasta refMrna.fa.gz is here: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/

Best, Jen, Galaxy team

ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

21 months ago by

csm165 • 0

United States

csm165 • 0 wrote:

Hello, Do you have any plans to change the interface for sailfish? Currently it says to either pick a genome from you history or use a built-in one, and if the genome you want isn't available to contact a galaxy admin. I'm sure you would save a bunch of people time and a bunch of emails to you guys if you made it clear that no built-in genomes will be available and/or remove that option.

Thanks, Chris

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