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Salmon Bam Quant Specifications

Process Details

  • Name: salmon_bam_quant
  • Process UUID: TbvBI63h5DoNXlsHQPR78vMTip8R8n
  • Process Group: Transcript Quant.

Overview

This process performs transcript quantification from BAM files using Salmon's quantification algorithm. It processes aligned RNA-seq reads to estimate transcript abundances, generating quantification results that can be used for downstream differential expression analysis and other transcriptomic studies.

This process is implemented in Bash, which invokes Salmon and other bioinformatics tools for transcript quantification from aligned sequencing data.

Key Functionality

  • Transcript Extraction: Extracts transcript sequences from the reference genome using the provided GTF annotation file
  • BAM-based Quantification: Quantifies transcript abundances directly from aligned BAM files using Salmon's quasi-mapping approach
  • Library Type Detection: Automatically infers or uses specified library strandedness and orientation parameters
  • Output Formatting: Generates standardized abundance files compatible with downstream analysis tools

Input/Output Specification

Inputs

Required Inputs

  • Mate Information

    • Description: Sample metadata and pairing information for the sequencing data
    • Format: Metadata value

  • GTF Annotation File

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

  • Reference Genome

    • Description: Reference genome sequence in FASTA format used for transcript extraction
    • Format: FASTA file

  • Mapped Reads

    • Description: Set of aligned RNA-seq reads in BAM format from upstream alignment processes
    • Format: BAM files

  • Process Control

    • Description: Runtime parameter controlling whether the quantification process should execute
    • Format: Process control value

Outputs

  • Quantification Results
    • Description: Directory containing Salmon quantification outputs including transcript abundance estimates and processing logs
    • Format: Directory with abundance files and logs

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 preparation protocol and strandedness 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 filter_gtf_for_genes_in_genome.py
  • 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.