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RNAFramework Index Specifications

Process Details

  • Name: RNAFramework Index
  • Process UUID: b6bc9e5da6dc40e2a33ae5904ec7577d
  • Process Group: Index

Overview

This process creates bowtie or bowtie2 indexes for RNA sequencing data mapping using the RNAFramework toolkit. The process supports both custom index generation from FASTA genome files and utilization of prebuilt UCSC indexes for common model organisms.

This process is implemented in Bash, which utilizes RNAFramework's rf-index tool along with bowtie/bowtie2 indexing utilities.

Key Functionality

  • Index Generation: Creates bowtie or bowtie2 indexes from genome FASTA files for RNA mapping
  • Prebuilt Index Support: Downloads and configures prebuilt UCSC indexes for common organisms
  • Multi-indexer Compatibility: Supports both bowtie and bowtie2 indexing algorithms
  • Custom Reference Processing: Handles user-provided genome references and existing index files

Input/Output Specification

Inputs

Optional Inputs

  • genome

    • Description: Reference genome sequence in FASTA format for custom index generation
    • Format: FASTA

  • bowtieIndex

    • Description: Pre-existing bowtie index files
    • Format: bowtieIndex

  • bowtie2index

    • Description: Pre-existing bowtie2 index files
    • Format: bowtie2index

Outputs

  • bowtieIndex
    • Description: Generated or processed bowtie/bowtie2 index files ready for RNA mapping
    • Format: bowtieIndex

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Indexer

    • Description: Choose an indexer. Note: This should be the same as the choice in Mapper module, as well.
    • Available options: bowtie (default), bowtie2

  • Indexing method

    • Description: Choose the indexing method. RF-Indexer: Obtains prebuilt UCSC indexes or a server (host and port are required). Custom: The indexes are built with the chosen indexer (Bowtie or Bowtie2)
    • Available options: RF-Indexer (default), Custom

  • Host

    • Description: UCSC server hostname (Default: genome-mysql.cse.ucsc.edu) (--host)
    • Default value: genome-mysql.cse.ucsc.edu

  • Port

    • Description: UCSC server port (Default: 3306) (--port)
    • Default value: 3306

  • Index ID

    • Description: Choose of the below IDs: 1: For Homo sapiens ribosomal RNAs [18S and 28S], 2: Mus musculus ribosomal RNAs [18S and 28S], 3: Saccharomyces cerevisiae ribosomal RNAs [18S and 25S], 4: Homo sapiens RefSeq Select and MANE RNAs [Assembly: hg38; Coding + non-coding], 5: Mus musculus RefSeq Select RNAs [Assembly: mm39; Coding + non-coding]. Default: 4
    • Available options: 1 (default), 2, 3, 4, 5

  • Genome assembly

    • Description: Genome assembly for the species of interest (Default: hg38)
    • Default value: hg38

References & Resources

  • Tool Documentation: Contact the team for details on RNAFramework indexing tools
  • Related Papers: Incarnato, D. et al. (2018). High-throughput single-base resolution mapping of RNA 2'-O-methylated residues. Nucleic Acids Research, 46(4), 1754-1767.