Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add bwa meth #159

Merged
merged 133 commits into from
Jun 8, 2020
Merged

Add bwa meth #159

merged 133 commits into from
Jun 8, 2020

Conversation

alexg9010
Copy link
Member

@alexg9010 alexg9010 commented Jun 3, 2020 •
edited
Loading

Major changes:

  • addition of a parallel workflow based on bwa-meth
  • addition of methylation caller methylDackel
  • post-mapping analysis depends more on methylKits tabix-based database files
  • layout of the differential analysis in the settings has been adapted from PiGx-RNAseq -
  • differential analysis report was update with a new quality control section, more context descriptions for the figures and the functionality to identify regions of similar differential methylation (DMRs)
  • add multiqc reports per pipeline branch (bismark and/or bwameth )

@alexg9010
update gitignore
e998a03
@alexg9010
add bwa-meth, bwa and sambamba as deps
1c8f8f8
@alexg9010
update gitignore
3203750
@alexg9010
add bwa-meth to pipeline
eec9728
@alexg9010
move guix.scm back to main folder
c6e0bcd
@alexg9010
Cut down Rules/Align_bwameth_rules
0a7b6f3 
- remove subsetting and filtering for now
- add link to kasias original file
- make rule accept paired and single end fastq
@alexg9010
more rules for processing bwameth output
850577a 
- add rules for marking duplicates and getting mapping stats
- rename Rules folder to rules
@alexg9010
force rerunning of incomplete rules
333fc9c
@alexg9010
update configure and makefile
4608a6b 
- add rule files for bwameth to makefile
- add samblaster as dependency
@alexg9010
Extract methylation from bwameth output
1911f15 
- add methylDackel as dependency
- extract methylation into methylKit format
- extract mbias from bwameth bam
- extract cytosine report from bwameth bam
- export tabix files for further use
@alexg9010
Export Bismark methCalls to tabix instead of RDS
4c57293 
- use methylKit to directly export to tabix for easier handling in later
rules
@alexg9010
inlude preprocessing rules in main SnakeFile
4ec2518
@alexg9010
export methylation signal from tabix to bigwig
526ef19
@alexg9010
export segmented methylation profile
dc9c4e3
@alexg9010
put sorted bam files into sorted folder
1863502
@alexg9010
export bigwig from tabix only
dfdf641
@alexg9010
missing slash in GENOMEPATH
6f5125c
@alexg9010
fix wildcard issue in methyldackel extract
6859d0b
@alexg9010
calculate diffmeth from tabix files
f88795c 
- introduce new rule unite to break process into smaller parts
- add functions to get files for rule_all
@alexg9010
missed a comma in unite rule
e4413fd
@alexg9010
changes to Differential Methylation Analysis
332d156 
- add support for many vs many comparison by reorganizing into treatment and
control
- put differential analysis into seperate section DManalysis
- allow for descriptive treatment groups
@alexg9010
reformat func_defs
a205003 
- update get_sampleids_from_analysis()
@alexg9010
update validation function
f7de185
@alexg9010
export some config vars as global vars
fb1bae6 
- export LOGOPATH, BIBTEXPATH, WEBFETCH, CPGISLAND_BEDFILE, REFGENES_BEDFILE
@alexg9010
add targets for either bismark or bwameth diffmeth report
3a99bc8
@alexg9010
move diffmeth rules to rules/perform_diffmeth.py
826e6e7
@alexg9010
adjust settings variable name
6692124
@alexg9010
update fetch procedures
e21634e 
- be more consistent for fetching from UCSC or AnnotationHub
- restrict possible tables
@alexg9010
render reports in explicit way
d670d33 
- remove generateReport()
- check report paramns and render report in generate_report.R
@alexg9010
update diffmeth report
89f7670 
- include sample pca
- show less tables
- recreate annotation figures using ggplot2
- distinguish between hypo and hyper methylation in TSS histogram
- add some explanations
- replace bibtex references with links to publications
rekado
rekado reviewed Jun 4, 2020
View reviewed changes
.gitignore Show resolved Hide resolved
BSseq_pipeline.py Outdated Show resolved Hide resolved
BSseq_pipeline.py Outdated Show resolved Hide resolved
BSseq_pipeline.py Show resolved Hide resolved
BSseq_pipeline.py Outdated Show resolved Hide resolved
scripts/methUnite.R Outdated Show resolved Hide resolved
tests/sample_sheet.csv Outdated Show resolved Hide resolved
tests/settings.yaml

general:
assembly: hg19
use_bwameth: True
# bismark is gold standard and uses sensible defaults
use_bismark: True
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Same comment as above about using "aligner:" instead.

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I would leave that open until we have #160 .

tests/settings.yaml Show resolved Hide resolved
tests/settings.yaml

withinGroup:
treatment_sample_groups: "MED2,MED1,H2O"
control_sample_groups: "MED2,MED1,H2O"
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

same as above on use of arrays.

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I would leave that open until we have #160 .

@alexg9010 alexg9010 merged commit 4431d00 into master Jun 8, 2020
This was referenced Jul 30, 2020
Closed
Closed
Closed
Closed
Closed
@alexg9010 alexg9010 deleted the add_bwa-meth branch July 30, 2020 12:12
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@rekado rekado rekado left review comments

@katwre katwre Awaiting requested review from katwre

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@alexg9010 @rekado