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Organize Kallisto Input Data

Description:

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: http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index.
  2. In the ‘Gene annotation’ section, click on the ‘Download genes, cDNAs, ncRNA, proteins’ ‘FASTA’ link: ftp://ftp.ensemblgenomes.org/pub/plants/release-36/fasta/arabidopsis_thaliana/.
  3. The transcriptome files will be located in the ‘cdna’ folder: ftp://ftp.ensemblgenomes.org/pub/plants/release-36/fasta/arabidopsis_thaliana/cdna/.
  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/Results

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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