View - Peaks or Signals: Different track formats often allow different views of the data of a single experiment. These views sometimes represent different stages of processing, such as experimental 'signal' resulting directly from high-throughput sequencing and called 'peaks' which result from further analysis.
ViewDescriptionLabel
Alignability Displays how uniquely k-mer sequences align to a region of the genome. The GEM mapper (GEnome Multitool, CRG) maps sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts) allowing up to 2 mismatches. Mappability scores were computed as S = 1/(number of matches found in the genome). The CRG Alignability tracks were generated independently of the ENCODE project. Alignability
Alignments Shows individual reads mapped to the genome and indicates where bases may mismatch Alignments
Base_Overlap_Signal An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Base overlap signal
Clusters Clusters built from the alignments Clusters
CNV Copy Number Variation CNV
Contigs Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). Contigs
CpG_Sites CpG Methylation Sites CpG Sites
Excludable Genomic regions for which mapped sequence tags were filtered out before signal generation and peak calling, problematic regions for short sequence tag signal detection (such as satellites and rRNA genes) Excludable
ExonsDeNovo Expression level estimates for Cufflinks exons, derived by summing the expression levels in RPKM for all transcripts containing a given exon ExonsDenovo
ExonsEnsV65IAcuff Expression level estimates for ENSEMBL V65 exons, and Cufflinks exons that are intergenic or antisense with respect to ENSEMBL 65 annotation. Exon RPKMs are computed by summing the expression levels in RPKM for all transcripts containing a given exon Exons ENSEMBL V65
ExonsGencV10 Expression level estimates for GENCODE V10 exons in gtf format derived by summing the expression levels in FPKM for all transcripts containing a given exon Exons Gencode V10
ExonsGencV3c Expression level estimates for GENCODE CRCh37.v3c exons in gtf format derived by summing the expression levels in FPKM for all transcripts containing a given exon Exons Gencode V3c
ExonsGencV7 Expression level estimates for GENCODE V7 exons in gtf format derived by summing the expression levels in FPKM for all transcripts containing a given exon Exons Gencode V7
Fasta3p 3 prime RNA FASTA Fasta3p
Fasta5p 5 prime RNA FASTA Fasta5p
FastaRd1 FASTA Read 1 FastaRd1
FastaRd2 FASTA Read 2 FastaRd2
FastqRd1 Raw sequence with Phred33 quality scores Read 1 FastqRd1
FastqRd2 Raw sequence with Phred33 quality scores Read 2 FastqRd2
FiltTransfrags Filtered transcript fragments Filtered Transfrags
GeneDeNovo 'De novo' genes defined by Cufflinks, and their associated RPKMs, as computed by the Flux Capacitor Genes De Novo
GeneEnsV65IAcuff Expression level estimates for ENSEMBL 65 genes, and Cufflinks gene models that are intergenic or antisense with respect to ENSEMBL 65 annotation Genes ENSEMBL V65
GeneGencV10 Expression level estimates at the gene level for the GENCODE V10 annotation in gtf format Genes Gencode V10
GeneGencV3c Expression level estimates at the gene level for the GENCODE CRCh37.v3c annotation in gtf format Genes Gencode V3c
GeneGencV7 Expression level estimates at the gene level for the GENCODE V7 annotation in gtf format Genes Gencode V7
HMM Hidden Markov Model HMM
Hotspots ChIP-seq affinity zones identified using the HotSpot algorithm Hotspots
Interactions ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. Interactions
Junctions TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Junctions
Matrix Interaction files in matrix format. The number of sequences mapped to each interaction fills the matrix. Matrix
MinusRawSignal Graphs the base-by-base density of tags on the minus strand Minus Raw signal
MinusSignal Graphs the base-by-base density of tags on the minus strand Minus signal
ModifiedPeptideMapping Modified Peptide Mapping Modified Peptide Mapping
mPepMapGcFt Modified peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. Modified Peptide Genome and GENCODE Mapping (filtered)
mPepMapGcUnFt Modified peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments unfiltered by false discovery rate (FDR). Modified Peptide Genome and GENCODE Mapping (unFiltered)
NonCpG_Sites Non-CpG Methylation Sites Non-CpG Sites
PctSignal Signal over an interval as a percentage of normalized tag densities over all phases Percentage-normalized Signal
Peaks Regions of enriched signal in experiment Peaks
pepMapFt Peptide mapping results based on the hg19 genome for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. Peptide Mapping (filtered)
pepMapGcFt Peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. Peptide Genome and GENCODE Mapping (filtered)
pepMapGcUnFt Peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments unfiltered by false discovery rate (FDR). Peptide Genome and GENCODE Mapping (unfiltered)
pepMapUnFt Peptide mapping results based on the hg19 genome for mass-spectrometry-based proteomics experiments unfiltered by false discovery rate (FDR). Peptide Mapping (unfiltered)
PeptideMapping PeptideMapping Peptide Mapping
PlusRawSignal Graphs the base-by-base density of tags on the plus strand Plus Raw signal
PlusSignal Graphs the base-by-base density of tags on the plus strand Plus signal
PrimerPeaks Regions of enriched signal for a given Primer Set Primer Peaks
Protocol Document of experimental methods Protocol
Qual3p Qual3p QUAL3P
Qual5p Qual5p Qual5p
RawData Sequence and quality files Raw data
RawData2 Sequence and quality files Raw data 2
RawSignal Shows the density of mapped reads on the plus and minus strands (wiggle format) Raw signal
RbpAssocRna Ribosome binding protein associated RNA Rbp Associated RNA
Regions Regions Regions
RepPeaks Peaks determined per individual replicate Replicate Peaks
RepSignal Signal determined per individual replicate Replicate Signal
Signal Signal Signal
SimpleSignal Simple Signal Simple Signal
Sites Sites Sites
SNP Single Nucleotide Polymorphism SNP
Spikeins Spikeins Spike-ins
Splices Subset of aligned reads that cross splice junctions Splices
SumSignal Shows summed densities of all phases combined Summed Densities
TranscriptDeNovo 'De novo' transcripts defined by Cufflinks, and their associated RPKMs, as computed by the Flux Capacitor Transcripts De novo
TranscriptEnsV65IAcuff Expression level estimates for ENSEMBL 65 transcript, and Cufflinks transcript models that are intergenic or antisense with respect to ENSEMBL 65 annotation Transcript ENSEMBL V65
TranscriptGencV10 Expression level estimates at the transcript level for the GENCODE V10 annotation in gtf format Transcript Gencode V10
TranscriptGencV3c Expression level estimates at the transcript level for the GENCODE CRCh37.v3c annotation in gtf format Transcript Gencode V3c
TranscriptGencV7 Expression level estimates at the transcript level for the GENCODE V7 annotation in gtf format Transcript Gencode V7
Transfrags Transcribed fragments Transfrags
TssGencV3c Expression level estimates for GENCODE v3c transcription start sites (TSS) in gtf format derived by summing the expression levels in FPKM for all transcripts originating from a given TSS TSS Gencode V3c
TssGencV7 Expression level estimates for GENCODE v7 transcription start sites (TSS) in gtf format derived by summing the expression levels in FPKM for all transcripts originating from a given TSS TSS Gencode V7
TssHmm Expression level estimates for transcription start sites (TSS) TSS HMM
UniformSignal Uniform Signal Uniform Signal by AWG
Uniqueness Displays how unique is each sequence on the positive strand starting at a particular base and of a particular length. The score of 1 represents completely unique, 0.5 occurs exactly twice, 0.33 three times, 0.25 four times and 0 occurs > 4 times (excluding chrN_random and alternative haplotypes). The Duke uniqueness tracks were generated for the ENCODE project. Uniqueness
Validation Documents used for the verification of experimental results Validation
Valleys Regions of enriched signal in experiment Valleys
WaveSignal Shows smoothed wavelet over all phases Wavelet-smoothed Signal

Total = 77