Resource
| Id | TF_ChIP-seq/ENCSR000AKB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000AKB [biosample_summary="Homo sapiens GM12878" and target="CTCF"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN637WKE|/analyses/ENCAN637WKE/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF389RQC|/files/ENCFF389RQC/} processed by ChIP-seq ENCODE3 hg19 pipeline has 6744960 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-human and investigated as a transcription factor is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/} ) audit_warning: Processed alignments file {ENCFF343LTM|/files/ENCFF343LTM/} processed by ChIP-seq ENCODE3 hg19 pipeline has 14330073 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-human and investigated as a transcription factor is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/} ) audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file {ENCFF389RQC|/files/ENCFF389RQC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.86. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed alignments file {ENCFF389RQC|/files/ENCFF389RQC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.76. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000AKB | float |
TF_ChIP-seq_ENCSR000AKB |
TF_ChIP-seq ENCSR000AKB [biosample_summary="Homo sapiens GM12878" and target="CTCF"]
|
 |
[3.9, 486] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12407139 | 0.39% | 41903 |
| chr1 | 1155245 | 0.46% | 3997 |
| chr2 | 969356 | 0.40% | 3222 |
| chr3 | 791704 | 0.40% | 2642 |
| chr4 | 602582 | 0.32% | 1954 |
| chr5 | 659579 | 0.36% | 2210 |
| chr6 | 734766 | 0.43% | 2450 |
| chr7 | 611468 | 0.38% | 2022 |
| chr8 | 550451 | 0.38% | 1810 |
| chr9 | 493908 | 0.36% | 1687 |
| chr10 | 587214 | 0.44% | 1978 |
| chr11 | 669940 | 0.50% | 2316 |
| chr12 | 635263 | 0.48% | 2159 |
| chr13 | 281635 | 0.25% | 926 |
| chr14 | 420058 | 0.39% | 1443 |
| chr15 | 402324 | 0.39% | 1393 |
| chr16 | 402351 | 0.45% | 1383 |
| chr17 | 548661 | 0.66% | 1933 |
| chr18 | 263328 | 0.33% | 866 |
| chr19 | 458695 | 0.78% | 1622 |
| chr20 | 335464 | 0.52% | 1162 |
| chr21 | 125544 | 0.27% | 416 |
| chr22 | 244951 | 0.48% | 851 |
| chrX | 462652 | 0.30% | 1461 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 41903 | 1 | 684 | 296.09 | 350 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF833FTF.bed.gz | 640.42 KB | 265cfe705263baae508111a4114aab61 |
| ENCFF833FTF.tabix.bed.gz | 492.01 KB | d83a5386e9db03efff7f1a9cdc7aaa08 |
| ENCFF833FTF.tabix.bed.gz.tbi | 261.6 KB | a37eef71ce99e818d719384c3497f7f0 |
| genomic_resource.yaml | 3.76 KB | bb69064af06f928e02fe4eaf23dfcb1c |
| statistics/ |