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Organize Kallisto Input Data


Kallisto has relatively few input requirements. You will need to have either single or paired end reads, as well as a reference transcriptome. It is suggested that your RNA-Seq reads are analyzed using FastQC, followed by any additional trimming and filtering using and application such as Trimmomatic.

Input Data:

Input Description Example
Reference transcriptome fasta Example transcriptome

Importing Reference Transcriptome

In this example, we will import a reference transcriptome for Arabidopsis from Ensembl. In many cases you can find an appropriate transcriptome from Ensembl for your organism of interest, or provide your own fasta-formmatted transcriptome.

  1. Go to the Ensembl Plants Arabidopsis page:
  2. In the ‘Gene annotation’ section, click on the ‘Download genes, cDNAs, ncRNA, proteins’ ‘FASTA’ link:
  3. The transcriptome files will be located in the ‘cdna’ folder:
  4. Right-click/command-click on the Arabidopsis_thaliana.TAIR10.cdna.all.fa.gz link and copy the link location/URL (usually right-click) to the clipboard
  5. Login to the CyVerse Discovery Environment.
  6. Open the Data window. In your home directory, create a folder to organize your Kallisto project
  7. In the created folder, go to the Data window’s ‘Upload’ menu, and select, ‘Import from URL…’; paste in the Ensembl link and click ‘Import from URL’ to begin the import


Output Description Example
Reference transcriptome fasta Example transcriptome

Description of results and next steps

This example transcriptome will be indexed in the next step. RNA-Seq reads will be mapped against this set of transcripts. Once you have the transcriptome and your RNA-Seq reads, you can proceed with the next step. We suggest organizing your RNA-Seq reads in the folder created in step 6 above.

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