MuG - FASTQ Pipelines’s documentation!

Contents:

• Requirements and Installation
  • Requirements
  • Installation
  • Documentation
• Full Installation
  • Setup the System Environment
  • Setup pyenv and pyenv-virtualenv
  • Installation Process
  • Setup the symlinks
  • Prepare the Python Environment
  • Post Installation Tidyup
• Pipelines
  • Download and index genome files
  • BioBamBam Alignment Filtering
  • Bowtie2 Alignment
  • BSgenome Builder
  • BS Seeker2 Indexer
  • BS Seeker2 Aligner
  • BiSulphate Sequencing Filter
  • BS Seeker2 Methylation Peak Caller
  • BWA Alignment - bwa aln
  • BWA Alignment - bwa mem
  • ChIP-Seq Analysis
  • iDamID-Seq Analysis
  • iNPS
  • MACS2 Analysis
  • Mnase-Seq Analysis
  • RNA-Seq Analysis
  • TrimGalore
  • Whole Genome BiSulphate Sequencing Analysis
  • Hi-C Analysis
• Tools for processing FastQ files
  • File Validation
  • Indexers
  • Aligners
  • Filters
  • Peak Calling
  • Hi-C Parsing
• Utility Functions
  • Common Functions
  • Alignment Utilities
  • Bam Utilities
  • FASTQ Functions
• Continuous Integration with Travis
  • Getting Started
  • Making .travis.yml File
  • Making harness.sh File
  • Running Docker container
  • Setting up Shims
• Setting up and using a Docker Container
  • Our reason for using a container
  • Getting Started
  • Constructing a docker container
• Architectural Design Record
  • 2017-08-15 - Implementation of pigz
  • 2018-01-26 - Disable no-self-use for @tasks
  • 2018-02-28 - BAM Merge Strategy
  • 2018-04-26 - BAM Splitting
  • 2018-05-01 - Compression of FASTQ
  • 2018-05-09 - Handling aligner index decompression
  • 2018-05-22 - GEM Naming
  • 2018-05-22 - TrimGalore
  • 2018-05-31 - Public genomes and indexes
  • 2018-06-01 - Separated WGBS Code Testing
  • 2018-06-01 - Travis Caching
  • 2018-06-04 - Split the WGBS test scripts
  • 2018-06-05 - Use of the logger PROGRESS
  • 2018-06-14 - Paired end alignment
  • 2018-06-18 - Branch tidying during alignment
  • 2018-06-27 - Remove reads marked as duplicate by BioBamBam
  • 2018-07-11 - Changes FASTQ splitter file management
  • 2018-07-16 - Modified handling of file locations
  • 2018-08-02 - Added in Paired End BAM file handling for MACS2
  • 2018-07-16 - Modified handling of file locations
  • 2018-08-07 - Storing tool parameters as part of the metadata
  • 2018-08-07 - Extra output files from MACS2
  • 2018-08-13 - Normalised the use of OSError
  • 2018-08-15 - Use the config.json execution path
  • 2018-08-16 - Prevent further duplicate filtering by MACS2
  • 2018-09-04 - Adding functionality to bam_utils and MACS2
  • 2018-09-17 - Updates to tool and pipline run()
  • 2018-08-22 - Improvement of tadbit tools wrappers
  • 2018-09-25 - Converting the Kallisto TSV file to BED
  • 2018-10-18 - Multi File handling for the DamID-seq Pipeline
  • 2018-10-25 - WGBS Pipeline Create BigWig files as standard
  • 2018-10-31 - Modify the file names for docker script
  • 2018-11-08 - Modifications for the movement of files
  • 2018-11-16 - Reading of Gzipped FASTQ files
• License

Test Datasets:

• Testing
  • Sample Data
  • Pipelines
  • Tools
• Test Data for ChIP-seq pipeline
  • Prerequisites
  • Data set for genome file
• iDamID-Seq Test Data
  • Test Data
  • Method
  • Test Scripts
• Test Data for MNase-seq pipeline
  • Prerequisites
  • Data set for genome file
• Test Data for RNA-seq pipeline
  • Prerequisites
  • Data set for genome file
• WGBS Test Data
  • Test Data
  • Method
  • Test Scripts
• Hi-C Test Data
  • Test Data
  • Method
  • Test Scripts

Indices and tables

• Index
• Module Index
• Search Page