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Salmon Quant Specifications

Process Details

  • Name: salmon_quant
  • Process UUID: IyDQO3a3rj58khfK3BYqHorcGyNhw3
  • Process Group: Transcript Quant.

Overview

Salmon quant performs transcript-level quantification from RNA-seq data using the Salmon quasi-mapping algorithm. This process maps sequencing reads to a pre-built transcript index and estimates transcript abundances, providing fast and accurate quantification without the need for full genome alignment.

This process is implemented in Bash, which invokes Salmon for transcript quantification and SAMtools for BAM file processing.

Key Functionality

  • Transcript Quantification: Estimates transcript-level expression using Salmon's quasi-mapping algorithm
  • Library Type Detection: Automatically infers or uses specified library strandedness and orientation
  • BAM File Generation: Converts mapping output to sorted and indexed BAM format for downstream analysis
  • Gene-Level Mapping: Maps transcript quantifications to gene-level annotations using provided GTF file

Input/Output Specification

Inputs

Required Inputs

  • Mate

    • Description: Sequencing library type specification (single or paired-end)
    • Format: Value specification

  • Reads

    • Description: RNA-seq sequencing reads for quantification
    • Format: FASTQ files

  • Salmon Index

    • Description: Pre-built Salmon transcript index for quasi-mapping
    • Format: Directory containing index files

  • GTF File

    • Description: Gene transfer format file containing transcript and gene annotations
    • Format: GTF file

  • Genome Sizes

    • Description: Chromosome/contig size information for the reference genome
    • Format: Sizes file

  • Genome

    • Description: Reference genome sequence in FASTA format
    • Format: FASTA file

Outputs

  • Output Directory

    • Description: Directory containing Salmon quantification results including abundance estimates
    • Format: Directory

  • BAM File

    • Description: Sorted and indexed alignment file containing mapped reads
    • Format: BAM files

  • BAM Index

    • Description: Index file for the generated BAM file enabling efficient random access
    • Format: BAI file

Parameters & Settings

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

  • Salmon Parameters

    • Description: Additional command-line parameters for Salmon quantification
    • Default value: (empty)

  • Library Type

    • Description: Library strandedness and orientation specification. A = automatically infer the library type. Relative orientation options: I = inward, O = outward, M = matching. Protocol options: U = unstranded, S = stranded. Strand-specific options: F = read 1 comes from forward strand, R = read 1 comes from reverse strand
    • Available options: A (default), U, SF, SR, IS, IU, ISF, ISR, OS, OU, OSF, OSR, MS, MU, MSF, MSR

References & Resources

  • Tool Documentation: Contact the team for details on Salmon quantification implementation
  • Related Papers: Patro, R., Duggal, G., Love, M.I., Irizarry, R.A., & Kingsford, C. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods, 14(4), 417-419. doi:10.1038/nmeth.4197