Resource
| Id | TF_ChIP-seq/ENCSR000BQS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BQS [biosample_summary="Homo sapiens GM12878" and target="REST"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: File {ENCFF313CII|/files/ENCFF313CII/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_internal_action: Archived analysis {ENCAN442KTA|/analyses/ENCAN442KTA/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF894EID|/files/ENCFF894EID/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 9835931 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 {ENCFF569QEN|/files/ENCFF569QEN/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 12374820 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 {ENCFF569QEN|/files/ENCFF569QEN/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF569QEN|/files/ENCFF569QEN/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.45. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BQS | float |
TF_ChIP-seq_ENCSR000BQS |
TF_ChIP-seq ENCSR000BQS [biosample_summary="Homo sapiens GM12878" and target="REST"]
|
 |
[3.46, 521] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 1683585 | 0.05% | 6739 |
| chr1 | 158457 | 0.06% | 628 |
| chr2 | 121706 | 0.05% | 492 |
| chr3 | 99553 | 0.05% | 393 |
| chr4 | 62645 | 0.03% | 243 |
| chr5 | 100498 | 0.06% | 403 |
| chr6 | 98573 | 0.06% | 393 |
| chr7 | 77773 | 0.05% | 311 |
| chr8 | 74545 | 0.05% | 293 |
| chr9 | 63728 | 0.05% | 260 |
| chr10 | 71602 | 0.05% | 283 |
| chr11 | 79746 | 0.06% | 318 |
| chr12 | 87842 | 0.07% | 351 |
| chr13 | 33028 | 0.03% | 131 |
| chr14 | 51206 | 0.05% | 206 |
| chr15 | 53124 | 0.05% | 213 |
| chr16 | 69346 | 0.08% | 276 |
| chr17 | 79135 | 0.10% | 309 |
| chr18 | 33356 | 0.04% | 133 |
| chr19 | 87918 | 0.15% | 340 |
| chr20 | 51114 | 0.08% | 201 |
| chr21 | 10330 | 0.02% | 41 |
| chr22 | 29195 | 0.06% | 116 |
| chrEBV | 54833 | 31.91% | 262 |
| chrM | 7265 | 43.85% | 33 |
| chrX | 27067 | 0.02% | 110 |
| 3341 contigs with no values (186116108 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 6739 | 1 | 587 | 249.83 | 276 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF313CII.bed.gz | 117.85 KB | ca4db15a84a95381cc0cb84611326272 |
| ENCFF313CII.tabix.bed.gz | 80.17 KB | 5cfe80be1c36d8418a8b1d1a70ccf22d |
| ENCFF313CII.tabix.bed.gz.tbi | 59.06 KB | b5974b6548836e819dc40a26b09620ea |
| genomic_resource.yaml | 3.83 KB | f614d5a98d390f586914378e68a73e3a |
| statistics/ |