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bisulfite sequencing pipeline from fastq to methylation reports
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README.md

Copyright 2017-2018: Alexander Gosdschan, Katarzyna Wreczycka, Bren Osberg, Ricardo Wurmus. This work is distributed under the terms of the GNU General Public License, version 3 or later. It is free to use for all purposes.


Summary

PiGx BSseq is a data processing pipeline for raw fastq read data of bisulfite experiments; it produces reports on aggregate methylation and coverage and can be used to produce information on differential methylation and segmentation. It was first developed by the Akalin group at MDC in Berlin in 2017.

The figure below provides a schematic of the process.

Install

You can install this pipeline with all its dependencies using GNU Guix:

guix package -i pigx-bsseq

You can also install it from source manually. PiGx BSseq uses the GNU build system. If you want to install PiGx BSseq from source (you can find the latest release here), please make sure that all required dependencies are installed and then follow these steps after unpacking the latest release tarball:

./configure --prefix=/some/where
make install

Dependencies

By default, the configure script expects tools to be in a directory listed in the PATH environment variable. For reproducibility We recommend installing the necessary tools with GNU Guix. If the tools are installed in a location that is not on the PATH you can tell the configure script about them with variables. Run ./configure --help for a list of all variables and options.

The following tools must be available:

All of these dependencies must be present in the environment at configuration time.

Installation of dependencies via Guix

Rather than installing all required packages manually, we generally recommend using GNU Guix. The following command spawns a sub-shell in which all dependencies are available:

guix environment -l guix.scm

Getting started

To run PiGx BSseq on your experimental data, first enter the necessary parameters in the spreadsheet file (see following section), and configure the appropriate settings in settings files; then, from the terminal type:

$ ./pigx-bsseq [options] sample_sheet.csv -s settings.yaml

To see all available options add the --help option to the above command

$ ./pigx-bsseq --help

usage: pigx-bsseq [-h] [-v] -s SETTINGS [-c CONFIGFILE] [--target TARGET] [-n] [--graph GRAPH] [--force] [--reason]
                  [--unlock]
                  sample_sheet

PiGx BSseq Pipeline.

PiGx BSseq is a data processing pipeline for raw fastq read data of
bisulfite experiments.  It produces methylation and coverage
information and can be used to produce information on differential
methylation and segmentation.

positional arguments:
  sample_sheet                             The sample sheet containing sample data in CSV format.

optional arguments:
  -h, --help                              show this help message and exit
  -v, --version                           show program's version number and exit
  -s SETTINGS, --settings SETTINGS        A YAML file for settings that deviate from the defaults.
  -c CONFIGFILE, --configfile CONFIGFILE  The config file used for calling the underlying snakemake process.  By
                                          default the file 'config.json' is dynamically created from the sample
                                          sheet and the settings file.
  --target TARGET                         Stop when the named target is completed instead of running the whole
                                          pipeline.  The default target is "final-report".  Pass "--target=help"
                                          to describe all available targets.
  -n, --dry-run                           Only show what work would be performed.  Do not actually run the
                                          pipeline.
  --graph GRAPH                           Output a graph in PDF format showing the relations between rules of
                                          this pipeline.  You must specify a graph file name such as
                                          "graph.pdf".
  --force                                 Force the execution of rules, even though the outputs are considered
                                          fresh.
  --reason                                Print the reason why a rule is executed.
  --unlock                                Recover after a snakemake crash.
  --verbose                               Print supplementary info on job execution.
  --printshellcmds                        Explicitly print commands being executed by snakemake to standard out.



This pipeline was developed by the Akalin group at MDC in Berlin in 2017-2018.

Input Parameters

The pipeline expects two kinds of input: a sample sheet in CSV format and a settings file specifying the desired behaviour of PiGx BSseq. PiGx BSseq will automatically generate a JSON configuration file from these inputs.

Sample Sheet

The sample sheet is a table with sample-specific information containing the names of fastq files, unique sample ids, the type of bisulfite sequencing experiment (such as RRBS or WGBS, currently, only WGBS is available) and treatment group for differential methylation detection.

An example sample sheet is provided in tests/sample_sheet.csv and contains the following:

Read1,Read2,SampleID,Protocol,Treatment
PE_1.fq.gz,PE_2.fq.gz,PEsample,WGBS,0
SE_techrep1.fq.gz,,SEsample,WGBS,1
SE_techrep2.fq.gz,,SEsample_v2,WGBS,2

In the same folder, sample\_sheet.ods is provided to allow for input specification in the Libre Office Spreadsheet package, or similar Excel-like programs. Once this spreadsheet is saved, select Save As-> Text CSV (.csv), and select the option to edit filters to ensure that fields are separated by a comma (i.e. Field delimiter = ',')

Settings File

The default settings file can be found at etc/settings.yaml; the values here are used for any settings that are not specified by the user in the main settings file (which override the defaults). An example settings file is provided in tests/settings.yaml with the following content

locations:
  input-dir: in/
  output-dir: out/
  genome-dir: genome/

general:
  assembly: hg19
  methylation-calling:
    minimum-coverage: 0
    minimum-quality: 10
  differential-methylation:
    cores: 20
    treatment-groups:
      - ['0', '1']
      - ['0', '2']
    annotation:
      cpgIsland_bedfile: genome/cpgIslandExt.hg19.bed.gz
      refGenes_bedfile:  genome/refGene.hg19.bed.gz
      webfetch:   no

execution:
  submit-to-cluster: no
  jobs: 6
  nice: 19
  cluster:
    memory: 8G
    stack: 128M
    queue: all
    contact-email: none

Note that indentation implies hierarchical structure; the significance of each section is discussed below.

Available settings

PiGx BSseq recognizes four sections in the settings file:

  • locations for input, output, and genome directories
  • general for general settings
  • execution for settings affecting the pipeline execution

Locations

Variable name description
input-dir string: location of the experimental input data files (currently requires .fastq.gz)
output-dir string: ultimate location of the output data and report files
genome-dir string: location of the reference genome data for alignment

All input files (paired- or single-end) must be present in the folder input-dir. All output produced by the pipeline will be written to the folder output-dir, with subdirectories corresponding to the various stages of the process. The directory genome-dir must contain the reference genome being mapped to. If genome-dir contains a pre-existing sub-directory called Bisulfite\_Genome, then the bisulfite-converted genome contained therein will be used for mapping. If this sub-directory does not exist, then the pipeline will perform this conversion itself (and will require permission to write to disk at the location genome-dir in order to create this sub-directory, otherwise an error will be raised.)

General

general:
  assembly: hg19
  methylation-calling:
    minimum-coverage: 0
    minimum-quality: 10
  differential-methylation:
    cores: 20
    treatment-groups:
      - ['0', '1']
    annotation:
      cpgIsland_bedfile: genome/cpgIslandExt.hg19.bed.gz
      refGenes_bedfile:  genome/refGene.hg19.bed.gz
      webfetch:   no
Variable name description
assembly string: UCSC assembly release name e.g. "hg19"
methylation-calling:minimum-coverage integer: Minimum read coverage to be included in the methylKit objects. Defaults to 1. Any methylated base/region in the with fewer hits than this value will be ignored.
methylation-calling:minimum-quality integer: Minimum phred quality score to call a methylation status for a base. Defaults to 10.
differential-methylation:cores integer: Denotes how many cores should be employed in parallel differential methylation calculations
differential-methylation:treatment-groups Array of strings indicating which groups (the "Treatment" column in the sample sheet) ought to be compared against one-another in differential methylation. The index corresponding to the control group must be entered first, followed by the 'treatment' under consideration. If differential methylation is to be omitted, remove this variable entirely from the settings file.
differential-methylation:annotation Annotation files for differential methylation, based on CpG islands and reference genes respectively.
webfetch Boolean: Should pigx download these annotation files from the internet if they are not found in the locations specified? (if no, then these sections are simply ommitted.)

Execution

execution:
  submit-to-cluster: no
  jobs: 6
  nice: 19
  cluster:
    memory: 8G
    stack: 128M
    queue: all.q
    contact-email: none
Variable name description
submit-to-cluster string: Whether the pipeline should run locally ("no") or on a cluster with an SGE queueing system ("yes").
jobs string: Number of jobs sent to cluster, e.g. "6"
nice integer: From -20 to 19; higher values make the program execution less demanding on computational resources
cluster:memory string: Amount of memory used for all jobs besides bismark, e.g. "8G"
cluster:stack string: Stack size limit (used for cluster jobs), e.g. "128m"
cluster:contact-email string: Email address where information about pipelines progress is sent (if it is running on a cluster).

Further values can be supplied. For example, should the user wish to allocate job submission onto a specific queue (which we will call X) for all rules being executed, they may set:

execution:
  ...
  cluster:
    queue:  X
  ...
...

Or certain rules can be allocated to specific queues as follows:

execution:
  ...
  rules:
    __default__:
      queue: X
    bismark_align_and_map_se:
      queue: Y
    ...
...

In the latter case, the __default__ rule must be defined, and there may not be any multiply-defined variables.

Tools

The values for the executable field for each tool are determined at configure time and usually won't have to be changed unless you want to experiment with a custom variant of a particular tool.

The args field for each tool accepts a string for additional arguments to be passed to the specified tool.

The bismark tool supports additional settings, such as cores (the number of cores used by bismark) and memory for the amount of RAM that bismark may use.

Running the pipeline

Once the sample sheet and settings file have been prepared, it may be useful to submit the pipeline with the dry-run argument shown above, to confirm execution will run. Once a run is submitted using the commands above, the config.json file will be automatically generated, and the unicode PiGx logo should appear. Sub-diretories will also be created in the output folder with names that are (approximately) sequentially-ordered to indicate their place in the sequence of operations. If a run is interuppted, it may be necessary to run the submission script with the option --unlock before resuming from where the previous run was terminated. PiGx generates its own documentation to screen during execution, however, the underlying process based on snakemake will produce further updates to screen showing the status of the run. Within each subfolder, further programs will generate their own log files that can be consulted in case debugging is necessary (e.g. if a run fails with a cryptic error message, and the output directory contains folders named 01_*, 02_*, 03_*, etc., we recommend reading the last few lines of the *.log files in the last directory to be created.)

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