1 Original mapping provided by Array Vendor Vendor mapping 1 \N 2 Raw value Raw value 1 \N 3 Generalised log transformation based on VSN variance stabilised scores VSN_GLOG 1 \N 6 Remapping to new assembly performed by LiftOver LiftOver 1 \N 7 Hidden Markov Model based predictions based on tiling array data Nessie (TilingHMM) 1 \N 8 Ratio generated by standard Sanger PCR array processing SangerPCR 1 \N 11 Solexa clusters Parzen 1 \N 12 Solexa clusters from wiggle data Parzen 1 \N 13 Custom hit list HitList 1 \N 15 Co-occurrence of overlapping feature types Co-occurrence Overlap 1 \N 16 {'reg_feats' => 'Features from Ensembl Regulatory Build.'} Regulatory Build 1 {"type" : "fg_regulatory_features", "name" : "Reg. Feats", "display" :"off", "depth" : 10, "default" : {"contigviewbottom" : "normal", "generegview" : "normal"} } 67 Tarbase miRNA target predictions TarBase 1 {"type" : "mirna_targets", "colourset" : "mirna", "display" :"off"} 19 VISTA is a resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. VISTA 1 {"type" : "regulatory_regions", "colourset" : "synteny", "display" :"off"} 22 Weighted mean standardisation using the one step Tukey Biweight algorithm Tukey Biweight 1 \N 121 Probe alignment Probe alignment 1 {"colourset" : "feature","type" : "_oligo","display" : "off","key" : "array_chip"} 122 Probe alignment Probe alignment 1 {"colourset" : "feature","type" : "_oligo","display" : "off","key" : "array_chip"} 14 Hidden Markov Model based predictions based on tiling array data HMM predictions based on tiling array data 1 {"type" : "ctcf", "name" : "CTCF", "display" : "off", "renderers" : {"off" : "Off", "tiling" : "Normal"} } 41 SWEmbl Peak Caller SWEmbl 1 \N 42 SWEmbl Peak Caller SWEmbl 1 \N 24 SWEmbl Peak Caller SWEmbl 1 \N 23 SWEmbl Peak Caller SWEmbl 1 \N 135 BWA single read alignment BWA 1 \N 46 SWEMBL Peak Caller SWEmbl 1 \N 47 SWEMBL Peak Caller SWEmbl 1 \N 10 Genomic alignments for arrays AlignProbe 0 \N 44 SWEMBL Peak Caller tuned for DNase1 SWEmbl 1 \N 164 Microarray probes from manufacturers are aligned to the genome by Ensembl, if the probe sequences are provided. The mapping is a two-step procedure outlined here. Probe2Transcript Annotation 0 \N 48 Manual Annotation Manual Annotation 1 \N 51 CCAT Peak Caller CCAT 1 \N 90 Reduced Representation Bisulphite Sequencing: 5 Methyl Cytosine (and 5hmC). Merged replicates and 0.0001 false discovery rate. RRBS 1 {} 91 Whole Genome Bisulphite Sequencing: 5 Methyl Cytosine (and 5hmC). Merged replicates and 0.0001 false discovery rate. WGBS 1 {} 69 SWEmbl Peak Caller with IDR peak filtering SWEMBL IDR 1 \N 70 Position Frequency Matrices from the Jaspar Database (5.0) Jaspar 0 \N 71 Fantom 5 TSS/Enhancer Predictions Fantom 5 1 {"type" : "regulatory_regions", "colourset" : "fantom", "display" :"off", "priority" : ["FANTOM robust enhancer"] } 61 Chromatin Immunoprecipitation Sequencing ChIP-Seq 1 \N 62 DNase I hypersensitive sites sequencing DNase-Seq 1 \N 64 Formaldehyde-Assisted Isolation of Regulatory Elements FAIRE-Seq 1 \N 38 SWEMBL Peak Caller SWEmbl 1 \N 39 SWEMBL Peak Caller SWEmbl 1 \N 40 SWEMBL Peak Caller SWEmbl 1 \N 68 SWEMBL Peak Caller SWEmbl 1 \N 115 samtools flagstats run for qc purposes samtools flagstats 0 \N 116 Computes enrichment and quality measures and fragment lengths for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data phantom peak quality tools 0 \N 117 Chance 0 \N 118 Computation of the proportion of reads in peaks Proportion of reads in peaks 0 \N 119 NGG CRISPR sites identified by the Wellcome Trust Sanger Institute Genome Editing (WGE) resource https://doi.org/10.1093/bioinformatics/btv308, with percent in-frame and favoured mutations as predicted by FORECasT https://doi.org/10.1038/nbt.4317. CRISPR SpCas9 1 \N 120 Segmentation of an epigenome Segmentation 1 \N