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Software and tools
supermaxiste edited this page Nov 12, 2019
·
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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 | 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 |
All parameters were set to default.
Parameter | Type | Description | |
---|---|---|---|
fastqc | -t |
flexible | Number of cores to use |
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) |
Parameter | Type | Description | |
---|---|---|---|
multiqc | -f |
fixed | Overwrites conflicting reports |
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 |
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 |
Website | Paper | Author(s) | |
---|---|---|---|
bedtools | π | π° | Quinlan et al. |
Bismark | π | π° | Krueger et al. |
dmrseq | π | π° | Korthauer et al. |
FastQC | π | π° | Simon Andrews |
EAGLE-RC | π | π° | Tony Kuo |
MultiQC | π | π° | Ewels et al. |
samtools | π | π° | Li et al. |
Trim Galore | π | π° | Felix Krueger |
qualimap | π | π° | GarcΓa-Alcalde et al. |
Advanced information to better understand & modify the workflow:
- Snakefile (rules and relationships)
- Scripts
- Software and tools