GitHub - katsikora/WGBS_analysis

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Name		Name	Last commit message	Last commit date
Latest commit History 15 Commits
.gitignore		.gitignore
170712sikora.WGBSpipe.userGuide.pdf		170712sikora.WGBSpipe.userGuide.pdf
BS_DMR_WGBS.py		BS_DMR_WGBS.py
BS_DMR_WGBS.py~		BS_DMR_WGBS.py~
BSmapWGBS.py		BSmapWGBS.py
BSmapWGBS.pyc		BSmapWGBS.pyc
BSmapWGBS.py~		BSmapWGBS.py~
BSmethXT_WGBS.py		BSmethXT_WGBS.py
BSmethXT_WGBS.pyc		BSmethXT_WGBS.pyc
BSmethXT_WGBS.py~		BSmethXT_WGBS.py~
BSmetricsWGBS.py		BSmetricsWGBS.py
BSmetricsWGBS.pyc		BSmetricsWGBS.pyc
BSmetricsWGBS.py~		BSmetricsWGBS.py~
BSprecut.py		BSprecut.py
BSprecut.pyc		BSprecut.pyc
BSprecut.py~		BSprecut.py~
BSrefprep.py		BSrefprep.py
BSstats_WGBS.py		BSstats_WGBS.py
BSstats_WGBS.pyc		BSstats_WGBS.pyc
BSstats_WGBS.py~		BSstats_WGBS.py~
README.txt		README.txt
README.txt~		README.txt~
WGBS_QC_report_template.Rmd		WGBS_QC_report_template.Rmd
WGBS_QC_report_template.Rmd~		WGBS_QC_report_template.Rmd~
WGBS_pipe_lite.py		WGBS_pipe_lite.py
WGBS_pipe_lite.py~		WGBS_pipe_lite.py~
WGBSpipe.POM.filt.R		WGBSpipe.POM.filt.R
WGBSpipe.POM.filt.R~		WGBSpipe.POM.filt.R~
WGBSpipe.interval_stats.limma.R		WGBSpipe.interval_stats.limma.R
WGBSpipe.interval_stats.limma.R~		WGBSpipe.interval_stats.limma.R~
WGBSpipe.metilene_stats.limma.R		WGBSpipe.metilene_stats.limma.R
WGBSpipe.singleCpGstats.limma.R		WGBSpipe.singleCpGstats.limma.R
WGBSpipe.singleCpGstats.limma.R~		WGBSpipe.singleCpGstats.limma.R~
WGBSpipe_example_wrapper.sh		WGBSpipe_example_wrapper.sh
downsample_se_pe.sh		downsample_se_pe.sh

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############################################################################
20180226
####v1.0.0
-the pipeline is now available in the 'lite' version i.e. with hardcoded software choices
-read mapping is done with bwa-meth, methylation extraction with MethylDackel, stats with limma, DMR calling with metilene
-functionality of trimReads has been modified: defaults to None (no read trimming). Other choices are: 'auto' - illumina adapter trimming with auto-detected 5'end hard-trimming or 'user' with user-supplied arguments to cutadapt.