Software and tools

This section goes through the tools used and specifies which parameters are flexible (modifiable via config.yaml) and which are fixed. All unmentioned parameters are not defined and input/output parameters are not mentioned either. For tools such as bedtools and samtools that are used for data wrangling, specifications are needless. In a second section there's an overview of the tools with useful links.

Parameter settings

Bismark

	Parameter	Type	Description
bismark	--prefix	fixed	Add prefix to output names
	--multicore	flexible	Number of cores to use
	--temp_dir	fixed	Location where to store temporary files
deduplicate_bismark	-p	fixed	Specifies if data is Paired-End
	-s	fixed	Specifies if data is Single-End
bismark_methylation_extractor	-p	fixed	Specifies if data is Paired-End
	-s	fixed	Specifies if data is Single-End
	--multicore	fixed	Number of cores to use
	--no_overlap	fixed	Avoid double scoring for Paired-End data
	--comprehensive	fixed	Merge strand-sepcific info into context-specific info
	--bedGraph	fixed	Produce bedGraph file with cytosine position and methylation state
	--CX	fixed	Output information from all cytosines irrespective of context
	--multicore	flexible	Number of cores to use
	--gzip	fixed	Output will be compressed in gzip format
coverage2cytosine	-CX	fixed	Output information from all cytosines irrespective of context

dmrseq

All parameters were set to default.

FastQC

	Parameter	Type	Description
fastqc	-t	flexible	Number of cores to use

EAGLE-RC

	Parameter	Type	Description
eagle-rc	--ngi	fixed	No genotype information available
	--phred64	flexible	PHRED score scale
	--paired	fixed	Specifies if data is Paired-End
	--bs=3	fixed	Accounts for bisulfite conversion (C-T and G-A are matches)

MultiQC

	Parameter	Type	Description
multiqc	-f	fixed	Overwrites conflicting reports

Trim Galore

	Parameter	Type	Description
trim_galore	-q 20	fixed	Default quality threshold
	--clip_R1	flexible	Cut bases from 5' of R1
	--clip_R2	flexible	Cut bases from 5' of R2
	--three_prime_clip_R1	flexible	Cut bases from 3' of R1
	--three_prime_clip_R2	flexible	Cut bases from 5' of R2
	--length 20	fixed	Default length threshold
	--phred33	fixed	PHRED quality score scale
	--paired	fixed	Specifies if data is Paired-End

qualimap

	Parameter	Type	Description
qualimap	-nt	flexible	Number of cores to use
	--java-mem-size=4G	fixed	Set memory limit to avoid problems with big bam files

Software references and links

	Website	Paper	Author(s)
bedtools	🌏	📰	Quinlan et al.
Bismark	🌏	📰	Krueger et al.
dmrseq	🌏	📰	Korthauer et al.
FastQC	🌏	📰	Simon Andrews
EAGLE-RC	🌏	📰	Tony Kuo
MultiQC	🌏	📰	Ewels et al.
samtools	🌏	📰	Li et al.
Trim Galore	🌏	📰	Felix Krueger
qualimap	🌏	📰	García-Alcalde et al.

Wiki index

1. Overview
2. Input files
3. Configuration file
4. Running Snakemake
5. Output structure

Advanced information to better understand & modify the workflow:

6. Snakefile (rules and relationships)
7. Scripts
8. Software and tools