diff --git a/docs/quantification/chip-seq/CHPv5.xml b/docs/quantification/chip-seq/CHPv5.xml
index 8f92919..942f1a2 100644
--- a/docs/quantification/chip-seq/CHPv5.xml
+++ b/docs/quantification/chip-seq/CHPv5.xml
@@ -79,27 +79,29 @@
- QcSummary
- JSON
+ GALvX_QCSummary
+ JSON / txt
collection
The median insert size (field: insertSizeMedian) is extracted from the QC summary file.
+ Note that for compatibility with previous alignment processes, the QC summary files
+ may also have the old tabular / text-based format (field: PE_insertsize (mapq>0))
-
- blacklist_regions
- BED
- single
- Blacklist region
-
reference_genome
2bit
single
The reference genome file; see DCC/download/results/references/genomes
+
+ blacklist_regions
+ BED
+ single
+ Blacklist region
+
chromosome_sizes
TSV
@@ -107,7 +109,7 @@
2-column, tab-separated table of chromosome sizes for reference genome
- autosomal_regions
+ autosome_regions
BED
single
A file listing all autosomes as BED regions for filtering
@@ -115,13 +117,13 @@
- DEEPID.PROC.DATE.raw.bamcov
+ DEEPID.PROC.DATE.ASSM.raw.bamcov
bigwig
collection
Signal coverage track generated from raw BAM files
- DEEPID.PROC.DATE.filt.bamcov
+ DEEPID.PROC.DATE.ASSM.filt.bamcov
bigwig
collection
@@ -129,92 +131,91 @@
- DEEPID.PROC.DATE.ses-fc
+ DEEPID.PROC.DATE.ASSM.ses.log2-Input
bigwig
collection
- SES normalized fold-change signal
+ SES normalized signal-over-Input track
- DEEPID.PROC.DATE.cnt-fc
+ DEEPID.PROC.DATE.ASSM.cnt.log2-Input
bigwig
collection
- Read-count normalized fold-change signal
+ Read-count normalized signal-over-Input track
- DEEPID.PROC.DATE.gcfreq
+ DEEPID.PROC.DATE.ASSM.gcbias
svg
collection
GC bias plot based on raw BAM files
- DEEPID.PROC.DATE.gcfreq
+ DEEPID.PROC.DATE.ASSM.gcfreq
txt
collection
Obs./exp. GC read frequencies based on raw BAM files
- DEEPID.PROC.DATE.hhmm.emfit
+ DEEPID.PROC.DATE.ASSM.hhmm.emfit
PDF
collection
histoneHMM output visualizing the EM fit. Check this before using the histoneHMM output
- DEEPID.PROC.DATE.hhmm.out
+ DEEPID.PROC.DATE.ASSM.hhmm.out
zip
collection
Zip archive containing other histoneHMM output files (raw data files not needed by most users)
- DEEPID.PROC.DATE.macs.out
+ DEEPID.PROC.DATE.ASSM.macs.out
zip
collection
Zip archive containing other MACS output files (raw data files not needed by most users)
- DEEPID.PROC.DATE.hhmm.broad
+ DEEPID.PROC.DATE.ASSM.hhmm.broad
BED / broadPeak
collection
Histone and Input enriched regions called by histoneHMM
- DEEPID.PROC.DATE.macs.broad
+ DEEPID.PROC.DATE.ASSM.macs.broad
BED / broadPeak
collection
Histone enriched regions called by MACS
- DEEPID.PROC.DATE.macs.narrow
+ DEEPID.PROC.DATE.ASSM.macs.narrow
BED / narrowPeak
collection
Histone enriched regions called by MACS
- DEEPID.PROC.DATE.fgpr
+ DEEPID.PROC.DATE.ASSM.fgpr
SVG
single
Fingerprint plots based on raw BAM files
- DEEPID.PROC.DATE.qm-fgpr
+ DEEPID.PROC.DATE.ASSM.qm-fgpr
txt
single
Fingerprint quality metrics based on raw BAM files
- DEEPID.PROC.DATE.counts-fgpr
+ DEEPID.PROC.DATE.ASSM.counts-fgpr
tsv
single
Fingerprint raw counts based on raw BAM files
-
- DEEPID.PROC.DATE.auto.counts-summ
+ DEEPID.PROC.DATE.ASSM.auto.counts-summ
tsv
single
multiBamSummary raw counts based on filtered and autosome-restricted BAM files
- DEEPID.PROC.DATE.auto.summ
+ DEEPID.PROC.DATE.ASSM.auto.summ
npz
single
@@ -222,16 +223,26 @@
The format is a numpy compatible binary file.
-
+
+ DEEPID.PROC.DATE.ASSM.bamcorr
+ SVG
+ collection
+ Correlation heatmaps using Pearson and Spearman correlation measure
+
+
+ DEEPID.PROC.DATE.ASSM.corrmat
+ tsv
+ collection
+ Raw correlation matrices
+
-
bamCoverage
2.5.3
@@ -245,7 +256,7 @@
GALvX_Histone, GALvX_Input
@@ -257,7 +268,7 @@
@@ -272,10 +283,10 @@
2.5.3
no looping
@@ -321,7 +332,7 @@
2.5.3
@@ -338,10 +349,10 @@
2.5.3
no looping
@@ -370,7 +381,7 @@
3.0
GALvX_Histone
@@ -398,7 +409,7 @@
DEEPID.hmm.bed &&
- mv DEEPID-zinba-emfit.pdf {DEEPID.PROC.DATE.hhmm.emfit}
+ mv DEEPID-zinba-emfit.pdf {DEEPID.PROC.DATE.ASSM.hhmm.emfit}
]]>
DEEPID-regions.gff
@@ -409,7 +420,7 @@
3.0
GALvX_Histone
@@ -418,8 +429,6 @@
-zinba-params-em.txt, .txt
-
-
sambamba
0.6.6
@@ -432,7 +441,6 @@
DEEPID.tmp.filt.bam
Count number of reads overlapping peak regions, later used for FRiP score
-
bedtools
2.26.0
@@ -444,7 +452,6 @@
peak_file
Intersect all peak files with blacklist regions for flagging
-
bedtools
2.26.0
@@ -456,14 +463,13 @@
histoneHMM_peak_file
Intersect all histoneHMM peak files with Input peaks for flagging
-
Python
2.7.13
{DEEPID.PROC.DATE.macs.narrow} {DEEPID.PROC.DATE.macs.broad} {DEEPID.PROC.DATE.hhmm.broad}
+ > {DEEPID.PROC.DATE.ASSM.macs.narrow} {DEEPID.PROC.DATE.ASSM.macs.broad} {DEEPID.PROC.DATE.ASSM.hhmm.broad}
]]>
peak-file
@@ -473,7 +479,6 @@
standard broadPeak/narrowPeak format specifications.
-
sambamba
0.6.6
@@ -493,9 +498,9 @@
2.5.3
no looping
@@ -506,10 +511,10 @@
2.5.3
no looping