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Sequential Mapping Bam Count Specifications

Process Details

  • Name: Sequential Mapping Bam Count
  • Process UUID: 17fc5c0e-e169-11e9-be30-e0aab38271b1
  • Process Group: Misc.

Overview

This process performs alignment counting across multiple BAM files using bedtools multicov functionality. It reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in BED files, providing separate counts for each BAM file and each BED interval. The process supports strand-specific counting and can handle different mapping strategies including sense, antisense, and combined alignments.

This process is implemented in Bash, which invokes a Perl script for sequential mapping and counting operations.

Key Functionality

  • Multi-BAM Alignment Counting: Uses bedtools multicov to count overlapping alignments from multiple BAM files against BED intervals
  • Strand-Specific Analysis: Supports sense-only (-s) and antisense-only (-S) counting modes for directional RNA-seq data
  • Dynamic BED File Generation: Automatically creates BED files from FASTA sequences when not present
  • Multiple Aligner Support: Compatible with Bowtie, Bowtie2, and STAR aligner outputs
  • Deduplication Handling: Processes both regular and deduplicated BAM files
  • Flexible Reference Selection: Supports genome-wide and custom sequence mapping strategies

Input/Output Specification

Inputs

Required Inputs

  • BAM File

    • Description: Sorted and indexed BAM alignment file
    • Format: BAM

  • BAM Index

    • Description: Index file for the BAM alignment file
    • Format: BAI

  • Bowtie Index

    • Description: Bowtie aligner index files
    • Format: bowtieIndex

  • Bowtie2 Index

    • Description: Bowtie2 aligner index files
    • Format: bowtie2index

  • STAR Index

    • Description: STAR aligner index files
    • Format: starIndex

  • Common Database

    • Description: Directory containing reference sequences and annotation files
    • Format: directory

Outputs

  • Output File TSV
    • Description: Tab-separated file containing alignment counts for each sequence/interval with columns for ID, length, and counts from each BAM file
    • Format: TSV

References & Resources

  • Tool Documentation: Contact the team for details on the Perl counting script
  • Related Papers: Li, H. et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079.