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?

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1 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.

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

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


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