Methylation_pipeline_updates_to_output_files.xlsx

	A	B	C	D	E	F	G
1	Methylation Pipeline Sample Output Updates
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3	Updated or new file that does not change anything that used to be in the previous version
4	Updated file that is different than the previous version (see comments for difference)
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6	Pipeline step	output file name (old pipeline)	output file name (proposed new pipeline	file definition		old vs. new pipeline	comment
7	Raw Data	raw_multiqc.html	raw_multiqc_GLMethylSeq.html	raw MultiQC report html	combines all samples	same (minor name change)
8		raw_multiqc_data.zip	raw_multiqc_GLMethylSeq_data.zip	raw MultiQC data	combines all samples	same (minor name change)
9	Trimming/quality filtering	*.trimmed.fastq.gz	*.trimmed.fastq.gz	Trimmed fastq files	1 or 2 per sample	same
10		*trimming_report.txt	*trimming_report.txt	trimming report	1 / sample	same
11		trimmed_multiqc.html	trimmed_multiqc_GLMethylSeq.html	filtered MultiQC report html	combines all samples	updated	includes cutadapt trimming stats as well as FastQC stats on trimmed files
12		trimmed_multiqc_data.zip	trimmed_multiqc_GLMethylSeq_data.zip	filtered MultiQC data	combines all samples	updated	includes cutadapt trimming stats as well as FastQC stats on trimmed files
13	Alignment	*_report.txt	*_report.txt	Bismark alignment report	1 / sample	same
14		genomic_nucleotide_frequencies.txt		Bismark genomic frequencing file	1 / genome	not output (part of reference)	Specific to genome not sample, so not included with sample files in OSDR
15		*.nucleotide_stats.txt	*.nucleotide_stats.txt	sample specific nucleotide stats	1 / sample	same
16		*_sorted.bam	*_sorted.bam	aligned BAM sorted by coordinate	1 / sample	same
17		_bismark__qualimap directory	_bismark__qualimap directory	Qualimap report files	1 / sample	same
18	Deduplication	*.deduplicated.bam	*.deduplicated.bam	deduplicated BAM	1 / sample (optional)	fixed	Original pipeline had deduplication on coordinate-sorted files, which is not supported by bismark deduplication tool.
19		*.deduplication_report.txt	*.deduplication_report.txt	deduplication stats	1 / sample (optional)	fixed
20			*_sorted.deduplicated.bam	deduplicated BAM sorted by coordinate	1 / sample (optional)	new file	Can be provided instead of unsorted deduplicated file or in addition to unsorted dedup file.
21	Methylation extraction	CpG_context_*.txt.gz	CpG_context_*.txt.gz	methylation call file for CpGs	1 / sample	sorted by coordinate in previous, unsorted in new	Consequence of using unsorted BAM as input
22		CHH_context_*.txt.gz	CHH_context_*.txt.gz	methylation call file for CHH	1 / sample	sorted by coordinate in previous, unsorted in new	Consequence of using unsorted BAM as input
23		CHG_context_*.txt.gz	CHG_context_*.txt.gz	methylation call file for CHG	1 / sample	sorted by coordinate in previous, unsorted in new	Consequence of using unsorted BAM as input
24		*.bedGraph.gz	*.bedGraph.gz	methylation calls in bedgraph format	1 / sample	same
25		*.bismark.cov.gz	*.bismark.cov.gz	methylation coverage file	1 / sample	same
26		*M-bias.txt	*M-bias.txt	methylation bias plot data	1 / sample	same
27		*_splitting_report.txt	*_splitting_report.txt	methylation extraction report	1 / sample	same
28		*cytosine_context_summary.txt	*cytosine_context_summary.txt	context-specific methylation summary report	1 / sample	same
29		*CpG_report.txt.gz	*CpG_report.txt.gz	genome-wide CpG methylation report	1 / sample	same
30	Bismark Reports	*_report.html	*_report.html	individual sample report	1 / sample	same
31		bismark_summary_report.txt	bismark_summary_report.txt	combined bismark summary report	combines all samples	fixed	Previous pipeline did not rename methylation splitting_report.txt to match sorted BAM file name, so bismark2summary cannot find it and parse corrected methylation stats.
32		bismark_summary_report.html	bismark_summary_report.html	combined bismark summary report	combines all samples	fixed
33	Compile Alignment and Bismark QC		align_and_bismark_multiqc_GLMethylSeq.html	alignment stats MulitQC report	combines all samples	new file	Full alignment report with both qualimap and bismark alignment stats.
34			align_and_bismark_multiqc_GLMethylSeq_data.zip	alignment stats MulitQC report	combines all samples	new file
35	Annotation	reference-gene-to-transcript-map-GLmethylSeq.tsv		gene to transcript mapping file	1 / transcriptome	not output (part of reference)	Specific to transcriptome not sample, so not included with sample files in OSDR
36	Differential methylation analsyis	*sig-diff-methylated-bases.tsv	*sig-diff-methylated-bases.tsv	signif. Differentially methylated cytosines	1 / factor pair	same
37		*sig-diff-hypermethylated-bases.tsv	*sig-diff-hypermethylated-bases.tsv	cytosines with significantly elevated methylation	1 / factor pair	same
38		*sig-diff-hypomethylated-bases.tsv	*sig-diff-hypomethylated-bases.tsv	cytosines with significantly reduced methylation	1 / factor pair	same
39		*sig-diff-methylated-tiles.tsv	*sig-diff-methylated-tiles.tsv	signif. Differentially methylated tiles	1 / factor pair	same
40		*sig-diff-hypermethylated-tiles.tsv	*sig-diff-hypermethylated-tiles.tsv	tiles with significantly elevated methylation levels	1 / factor pair	same
41		*sig-diff-hypomethylated-tiles.tsv	*sig-diff-hypomethylated-tiles.tsv	tiles with significantly reduced methylation levels	1 / factor pair	same
42		base-level-percent-methylated.tsv	base-level-percent-methylated.tsv	% methylation levels of cytosines for all samples	combines all samples	same
43		tile-level-percent-methylated.tsv	tile-level-percent-methylated.tsv	% methylation levels of tiles for all samples	combines all samples	same
44		*sig-diff-methylated-bases-across-features.pdf	*sig-diff-methylated-bases-across-features.pdf	plot of % signif. Diffentially methylated cytosines in promoter, exon, intron	1 / factor pair	same
45		*sig-diff-methylated-tiles-across-features.pdf	*sig-diff-methylated-tiles-across-features.pdf	plot of % signif. Diffentially methylated tiles in promoter, exon, intron	1 / factor pair	same
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