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Check Build Kallisto Index Specifications

Process Details

  • Name: Check Build Kallisto Index
  • Process UUID: lytmajExsVDPbSJHusr0yvP7Lsyf6B
  • Process Group: Index

Overview

This process builds a Kallisto index for RNA-seq quantification using the provided genome FASTA file and GTF annotation file. The process performs necessary preprocessing steps to filter the GTF file, generate the transcriptome FASTA file, and then creates the Kallisto index. If the index file is not found, a new index directory is created, and if the index directory already exists, a symbolic link is established to it.

This process is implemented in Bash, which invokes Python scripts for GTF filtering and uses gffread for transcriptome extraction.

Key Functionality

  • GTF Filtering: Filters the GTF annotation file to include only genes present in the genome FASTA file
  • Transcriptome Extraction: Generates transcriptome FASTA sequences from the filtered GTF and genome files using gffread
  • Index Creation: Builds a Kallisto index from the transcriptome sequences with unique transcript handling

Input/Output Specification

Inputs

Required Inputs

  • Genome

    • Description: Reference genome sequence file
    • Format: FASTA

  • GTF File

    • Description: Gene annotation file containing transcript and exon information
    • Format: GTF

Outputs

  • Kallisto Index
    • Description: Kallisto index file for RNA-seq quantification
    • Format: IDX

Parameters & Settings

This process does not have user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on filter_gtf_for_genes_in_genome.py
  • Related Papers: Bray, N.L., Pimentel, H., Melsted, P. et al. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 34, 525–527 (2016). https://doi.org/10.1038/nbt.3519