use Kallisto in galaxy

Question

I want to use Kallisto for sequence alignment in Galaxy. Its description is:

a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

However, I found this field empty:

there is no option available for the reference transcriptome.

• How I use a reference sequence?
• Can I leave the other configuration by default?

• this is the link of the tool: https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3

Answer 1

You have to click on the dropdown menu and select "Use transcriptome from history", which will allow you to specify your own file.

I suspect the default will be built-in human transcriptome.

Solution is not tested, so let us know if it actually works.