Resource
| Id | TF_ChIP-seq/ENCSR000BJJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BJJ [biosample_summary="Homo sapiens SK-N-SH" and target="REST"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN120BZI|/analyses/ENCAN120BZI/} has in progress subobject document {35f4af5f-3e14-482f-bb41-dbd1fd1524a7|/documents/35f4af5f-3e14-482f-bb41-dbd1fd1524a7/} audit_internal_action: Released analysis {ENCAN120BZI|/analyses/ENCAN120BZI/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_not_compliant: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF358XFJ|/files/ENCFF358XFJ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 3.68 and a self consistency ratio of 5.56. According to ENCODE standards, having both rescue ratio and self consistency ratio values < 2 is recommended, but having only one of the ratio values < 2 is acceptable. audit_warning: Processed alignments file {ENCFF310DLW|/files/ENCFF310DLW/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 10566392 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 {ENCFF155PZC|/files/ENCFF155PZC/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 13651188 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/} ) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BJJ | float |
TF_ChIP-seq_ENCSR000BJJ |
TF_ChIP-seq ENCSR000BJJ [biosample_summary="Homo sapiens SK-N-SH" and target="REST"]
|
 |
[5.25, 455] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 2244569 | 0.07% | 9642 |
| chr1 | 220991 | 0.09% | 949 |
| chr2 | 192833 | 0.08% | 828 |
| chr3 | 123535 | 0.06% | 535 |
| chr4 | 83255 | 0.04% | 354 |
| chr5 | 124935 | 0.07% | 537 |
| chr6 | 106526 | 0.06% | 456 |
| chr7 | 162222 | 0.10% | 693 |
| chr8 | 86874 | 0.06% | 371 |
| chr9 | 92953 | 0.07% | 400 |
| chr10 | 110778 | 0.08% | 472 |
| chr11 | 130121 | 0.10% | 557 |
| chr12 | 102666 | 0.08% | 442 |
| chr13 | 41770 | 0.04% | 179 |
| chr14 | 58682 | 0.05% | 249 |
| chr15 | 73996 | 0.07% | 316 |
| chr16 | 85965 | 0.10% | 372 |
| chr17 | 146171 | 0.18% | 628 |
| chr18 | 41857 | 0.05% | 179 |
| chr19 | 96468 | 0.16% | 422 |
| chr20 | 72435 | 0.11% | 317 |
| chr21 | 16909 | 0.04% | 71 |
| chr22 | 47656 | 0.09% | 208 |
| chrX | 24971 | 0.02% | 107 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 9642 | 7 | 408 | 232.79 | 244 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF358XFJ.bed.gz | 172.2 KB | c05cae43de81338b910ee2ee56733ee4 |
| ENCFF358XFJ.tabix.bed.gz | 113.22 KB | d5374484c85b7ef382ca47a5bc998a27 |
| ENCFF358XFJ.tabix.bed.gz.tbi | 79.78 KB | 3a6224e658ae6d5e6784b935f9edb351 |
| genomic_resource.yaml | 3.26 KB | ad41347801b19c4bb993f317feafcfbc |
| statistics/ |