Resource
| Id | TF_ChIP-seq/ENCSR000BTF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BTF [biosample_summary="Homo sapiens HL-60" and target="REST"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN334XUB|/analyses/ENCAN334XUB/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-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 {ENCFF128UOK|/files/ENCFF128UOK/}, {ENCFF603MCO|/files/ENCFF603MCO/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 2.18 and a self consistency ratio of 4.32. 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_not_compliant: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF975OED|/files/ENCFF975OED/}, {ENCFF939MDW|/files/ENCFF939MDW/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 2.18 and a self consistency ratio of 4.32. 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 {ENCFF027GJA|/files/ENCFF027GJA/} processed by ChIP-seq ENCODE3 hg19 pipeline has 19132039 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_ENCSR000BTF | float |
TF_ChIP-seq_ENCSR000BTF |
TF_ChIP-seq ENCSR000BTF [biosample_summary="Homo sapiens HL-60" and target="REST"]
|
 |
[8.11, 694] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4872938 | 0.15% | 15002 |
| chr1 | 508028 | 0.20% | 1551 |
| chr2 | 377786 | 0.16% | 1178 |
| chr3 | 292021 | 0.15% | 883 |
| chr4 | 195099 | 0.10% | 595 |
| chr5 | 197825 | 0.11% | 594 |
| chr6 | 277930 | 0.16% | 864 |
| chr7 | 233182 | 0.15% | 736 |
| chr8 | 181704 | 0.13% | 565 |
| chr9 | 201049 | 0.15% | 640 |
| chr10 | 207942 | 0.16% | 639 |
| chr11 | 265689 | 0.20% | 800 |
| chr12 | 258512 | 0.19% | 792 |
| chr13 | 121571 | 0.11% | 381 |
| chr14 | 124096 | 0.12% | 378 |
| chr15 | 161088 | 0.16% | 495 |
| chr16 | 189431 | 0.21% | 568 |
| chr17 | 230496 | 0.28% | 708 |
| chr18 | 141081 | 0.18% | 440 |
| chr19 | 276276 | 0.47% | 865 |
| chr20 | 164913 | 0.26% | 511 |
| chr21 | 57142 | 0.12% | 174 |
| chr22 | 112328 | 0.22% | 342 |
| chrX | 97749 | 0.06% | 303 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 15002 | 3 | 890 | 324.82 | 390 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF603MCO.bed.gz | 244.39 KB | bd65a9b594a044fa6e72d0baca077e59 |
| ENCFF603MCO.tabix.bed.gz | 177.12 KB | c892f57e372f8ed152a186ac288265ba |
| ENCFF603MCO.tabix.bed.gz.tbi | 102.49 KB | ef36f564f59850725e4e048ef0b95fd2 |
| genomic_resource.yaml | 2.99 KB | 419a3fe3ee20487e17a2ffffa2834122 |
| statistics/ |