Resource
| Id | TF_ChIP-seq/ENCSR000BMN |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BMN [biosample_summary="Homo sapiens HeLa-S3" and target="REST"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: File {ENCFF208NUB|/files/ENCFF208NUB/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_internal_action: Archived analysis {ENCAN233HZE|/analyses/ENCAN233HZE/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF355WAL|/files/ENCFF355WAL/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 9245837 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting REST-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 {ENCFF754IAO|/files/ENCFF754IAO/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 12326841 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting REST-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 {ENCFF754IAO|/files/ENCFF754IAO/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. 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 {ENCFF754IAO|/files/ENCFF754IAO/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.20. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BMN | float |
TF_ChIP-seq_ENCSR000BMN |
TF_ChIP-seq ENCSR000BMN [biosample_summary="Homo sapiens HeLa-S3" and target="REST"]
|
 |
[3.48, 523] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 2768008 | 0.09% | 11871 |
| chr1 | 264242 | 0.11% | 1127 |
| chr1_KI270713v1_random | 244 | 0.60% | 1 |
| chr2 | 199168 | 0.08% | 862 |
| chr3 | 184792 | 0.09% | 790 |
| chr4 | 86869 | 0.05% | 377 |
| chr5 | 171119 | 0.09% | 732 |
| chr6 | 151182 | 0.09% | 650 |
| chr7 | 122026 | 0.08% | 530 |
| chr8 | 134779 | 0.09% | 579 |
| chr9 | 127097 | 0.09% | 538 |
| chr10 | 120684 | 0.09% | 513 |
| chr11 | 147918 | 0.11% | 640 |
| chr12 | 140876 | 0.11% | 610 |
| chr13 | 49989 | 0.04% | 218 |
| chr14 | 95592 | 0.09% | 411 |
| chr15 | 109719 | 0.11% | 464 |
| chr16 | 105067 | 0.12% | 454 |
| chr17 | 127232 | 0.15% | 540 |
| chr18 | 59508 | 0.07% | 261 |
| chr19 | 102962 | 0.18% | 426 |
| chr20 | 103473 | 0.16% | 432 |
| chr21 | 28495 | 0.06% | 124 |
| chr22 | 46146 | 0.09% | 197 |
| chrEBV | 28345 | 16.50% | 120 |
| chrM | 6029 | 36.39% | 28 |
| chrX | 54211 | 0.03% | 246 |
| chrY | 244 | <0.01% | 1 |
| 3339 contigs with no values (128847948 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 11871 | 7 | 574 | 233.17 | 244 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF208NUB.bed.gz | 193.63 KB | 3a0823a118dde65ca89700b16c8ff92a |
| ENCFF208NUB.tabix.bed.gz | 141.04 KB | 4e7936bf4009d121a227dd1769c6e5d0 |
| ENCFF208NUB.tabix.bed.gz.tbi | 99.52 KB | 49358ee30e1b63a34cde05bdd6c887c8 |
| genomic_resource.yaml | 3.83 KB | 43223a0d4422661fda5508c68a7042bf |
| statistics/ |