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Build Kallisto Transcriptome Index


As described in the Kallisto paper, RNA-Seq reads are efficiently mapped through a pseudoalignment process against a reference transcriptome index. We will build the index in this step.

Input Data:

Input Description Example
Reference transcriptome fasta Example transcriptome

Build Kallisto Index

We will now index the Arabidopsis transcriptome imported from Ensembl. This transcriptome can be used multiple times for future Kallisto analyses and only needs to be made once.

  1. If necessary, login to the CyVerse Discovery Environment.
  2. Open the Kallisto-0.42.3-index App.
  3. Name your analysis, and if desired enter comments. In the App's 'Input' step under 'Index name' enter a name for your index. For this tutorial, name your index Arabidopsis_thaliana.TAIR10.36.cdna.all.fa.index.
  4. For 'Fasta file' browse to the transcriptome imported in the previous section.
  5. If desired adjust the k-mer length (See Kallisto paper for recommendations); we will use the default.
  6. Click 'Launch Analyses' to start the job. Click on the Analyses button to monitor the job and results.


Output Description Example
Kallisto Index This is the index file Kallisto will map RNA-Seq reads to. Example Kallisto index

Description of results and next steps

With the index, we will now use the Kallisto Quant App to do a pesudoalignment of the RNA-Seq reads.

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