diff --git a/docs/quantification/chip-seq/CHPv5.xml b/docs/quantification/chip-seq/CHPv5.xml
index 9a828a6..3b97b0e 100644
--- a/docs/quantification/chip-seq/CHPv5.xml
+++ b/docs/quantification/chip-seq/CHPv5.xml
@@ -68,25 +68,82 @@
- DEEPID.PROC.DATE.ext
- EXT
+ DEEPID.PROC.DATE.raw.bamcov
+ bigwig
collection
- Process output not yet defined
+ Signal coverage track generated from raw BAM files
+
+ DEEPID.PROC.DATE.filt.bamcov
+ bigwig
+ collection
+
+ Signal coverage track generated from filtered BAM files. -F 3844 / q >= 5 / blacklist removed
+
+
+
+ DEEPID.PROC.DATE.ses-fc
+ bigwig
+ collection
+ SES normalized fold-change signal
+
+
+ DEEPID.PROC.DATE.cnt-fc
+ bigwig
+ collection
+ Read-count normalized fold-change signal
+
+
+ DEEPID.PROC.DATE.gcfreq
+ svg
+ collection
+ GC bias plot based on raw BAM files
+
+
+ DEEPID.PROC.DATE.gcfreq
+ txt
+ collection
+ Obs./exp. GC read frequencies based on raw BAM files
+
+
+ DEEPID.PROC.DATE.hhmm.emfit
+ PDF
+ collection
+ histoneHMM output visualizing the EM fit. Check this before using the histoneHMM output
+
+
+ DEEPID.PROC.DATE.hhmm.out
+ zip
+ collection
+ Zip archive containing other histoneHMM output files (raw data files not needed by most users)
+
+
+ DEEPID.PROC.DATE.fgpr
+ SVG
+ single
+ Fingerprint plots based on raw BAM files
+
+
+ DEEPID.PROC.DATE.qm-fgpr
+ txt
+ single
+ Fingerprint quality metrics based on raw BAM files
+
+
+
- plotFingerprint
+ bamCoverage
2.5.3
- no looping
- Compute fingerprint on raw BAM files
+ GALvX_Histone, GALvX_Input
+ Generate read coverage signal normalized to 1x depth for raw BAM files
computeGCBias
@@ -94,7 +151,7 @@
@@ -118,16 +175,17 @@
- bamCoverage
+ plotFingerprint
2.5.3
- GALvX_Histone, GALvX_Input
- Generate read coverage signal normalized to 1x depth for raw BAM files
+ no looping
+ Compute fingerprint on raw BAM files
@@ -135,7 +193,7 @@
0.6.6
= 5"
{GALvX_*}
]]>
@@ -145,31 +203,21 @@
Apply IHEC ChIP QC standard filtering to all BAM files (equivalent to bitflag 3844).
The resulting BAM files are temporary and discarded after the analysis.
-
-
- MACS2
- 2.1.1.20160309
-
-
-
- GALvX_Histone
- MACS2 peak calling on filtered BAM files. Parameter "--broad" for libraries H3K4me1/H3K27me3/H3K36me/H3K9me3
-
- histoneHMM
- 1.7
-
+ sambamba
+ 0.6.6
+
DEEPID.mapped.readcount
]]>
- GALvX_Histone
- HistoneHMM peak calling on filtered BAM files for broad marks: H3K4me1/H3K27me3/H3K9me3/H3K36me3
+ DEEPID.tmp.filt.bam
+
+ Due to the previous filtering step, counting simply all reads in the filtered BAM
+ file is equivalent to counting only mapped reads. The number of mapped reads is needed
+ to compute the FRiP score in a later stage.
+
bamCoverage
@@ -177,66 +225,66 @@
DEEPID.tmp.filt.bam
- Generate read coverage signal normalized to 1x depth for filtered BAM files
+
+ Generate read coverage signal normalized to 1x depth for filtered BAM files.
+ Remove blacklist regions on-the-fly and consider only autosomes for normalization step.
+
-
- multiBamSummary
+ plotFingerprint
2.5.3
no looping
- Create data matrix for correlation plot on filtered BAM files; remove blacklist regions on the fly
+ Compute fingerprint on filtered BAM files to compute IHEC QC measures
- plotCorrelation
- 2.5.3
+ MACS2
+ 2.1.1.20160309
- no looping
- Create heatmap correlation plot using Spearman and Pearson correlation
+ GALvX_Histone
+ MACS2 peak calling on filtered BAM files. Parameter "--broad" for libraries H3K27me3/H3K36me/H3K9me3
-
- plotFingerprint
- 2.5.3
+
+
+ histoneHMM
+ 1.7
- no looping
- Compute fingerprint on filtered BAM files; remove blacklist regions on the fly
+ GALvX_Histone
+ HistoneHMM peak calling on filtered BAM files for broad marks: H3K4me1/H3K27me3/H3K9me3/H3K36me3
- sambamba
- 0.6.6
+ cut, sort, mv
+ 8.13
DEEPID.hmm.bed &&
+ mv DEEPID-zinba-emfit.pdf DEEPID.PROC.DATE.hhmm.emfit.pdf
]]>
- DEEPID.tmp.filt.bam
-
- Get flagstat output for filtered BAM files, specifically number of mapped reads in these files.
- This is done to compute the IHEC QC metrics as part of this process.
-
+ DEEPID-regions.gff
+ Make histoneHMM output BED-like for blacklist intersection and standardize name of EM fit PDF.
+
sambamba
0.6.6
@@ -263,19 +311,46 @@
Values input from the two previous steps.
+
- bedtools
- 2.26.0
+ sambamba
+ 0.6.6
{DEEPID.PROC.DATE.peaks}
- ]]>
-
- All peak files
+ sambamba view --format=bam --nthreads={sambamba_parallel} --output-filename DEEPID.tmp.auto.bam
+ --regions={autosome_regions} DEEPID.tmp.filt.bam
+ ]]>
+
+ DEEPID.tmp.filt.bam
- Discard peaks overlapping with a known blacklist region after computing FRiP score.
- There does not seem to be an IHEC standard concerning this, correct?
+ Restrict filtered BAM files to autosomal regions. These BAM files will be used to plot the correlation heatmaps.
+
+ multiBamSummary
+ 2.5.3
+
+
+
+ no looping
+ Create data matrix for correlation plot on filtered BAM files; remove blacklist regions on the fly
+
+
+ plotCorrelation
+ 2.5.3
+
+
+
+ no looping
+ Create heatmap correlation plot using Spearman and Pearson correlation
+
+