Skip to content

Latest commit

 

History

History
106 lines (73 loc) · 2.92 KB

step1.rst

File metadata and controls

106 lines (73 loc) · 2.92 KB

_

Home_Icon_ Learning Center Home

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 , followed by any additional trimming and filtering using and application such as .


Input Data:

Input Description Example
Reference transcriptome fasta

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 .
  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

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.


Fix or improve this documentation

  • Search for an answer:
  • Ask us for help: click on the lower right-hand side of the page
  • Report an issue or submit a change:
  • Send feedback: Tutorials@CyVerse.org

Home_Icon_ Learning Center Home