Resource
| Id | TF_ChIP-seq/ENCSR000BGA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BGA [biosample_summary="Homo sapiens PFSK-1" and target="FOXP2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_error: Processed alignments file {ENCFF054FYX|/files/ENCFF054FYX/} processed by ChIP-seq ENCODE3 hg19 pipeline has 3695969 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting FOXP2-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_internal_action: Archived analysis {ENCAN379GUS|/analyses/ENCAN379GUS/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF320MKV|/files/ENCFF320MKV/} processed by ChIP-seq ENCODE3 hg19 pipeline has 8161038 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting FOXP2-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: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF395BZZ|/files/ENCFF395BZZ/}, {ENCFF260VMG|/files/ENCFF260VMG/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.59 and a self consistency ratio of 9.73. 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: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF794IDP|/files/ENCFF794IDP/}, {ENCFF299QQS|/files/ENCFF299QQS/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.59 and a self consistency ratio of 9.73. 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. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BGA | float |
TF_ChIP-seq_ENCSR000BGA |
TF_ChIP-seq ENCSR000BGA [biosample_summary="Homo sapiens PFSK-1" and target="FOXP2"]
|
 |
[2.27, 217] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5520408 | 0.17% | 20294 |
| chr1 | 502957 | 0.20% | 1854 |
| chr2 | 410277 | 0.17% | 1496 |
| chr3 | 218296 | 0.11% | 782 |
| chr4 | 143851 | 0.08% | 517 |
| chr5 | 281289 | 0.15% | 1033 |
| chr6 | 313900 | 0.18% | 1147 |
| chr7 | 268536 | 0.17% | 970 |
| chr8 | 306119 | 0.21% | 1132 |
| chr9 | 156072 | 0.11% | 575 |
| chr10 | 247687 | 0.19% | 900 |
| chr11 | 346896 | 0.26% | 1286 |
| chr12 | 237586 | 0.18% | 878 |
| chr13 | 77231 | 0.07% | 282 |
| chr14 | 119949 | 0.11% | 449 |
| chr15 | 238693 | 0.23% | 889 |
| chr16 | 182070 | 0.20% | 677 |
| chr17 | 422762 | 0.51% | 1559 |
| chr18 | 94705 | 0.12% | 339 |
| chr19 | 444613 | 0.76% | 1667 |
| chr20 | 182149 | 0.28% | 676 |
| chr21 | 78285 | 0.17% | 293 |
| chr22 | 168867 | 0.33% | 617 |
| chrX | 77618 | 0.05% | 276 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 20294 | 2 | 425 | 272.02 | 300 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF395BZZ.bed.gz | 295.48 KB | 4e19b95df0695a93ba3dc403d0d64995 |
| ENCFF395BZZ.tabix.bed.gz | 233.64 KB | ec3403fb1cbb6bf83f47f4dd82b53313 |
| ENCFF395BZZ.tabix.bed.gz.tbi | 126.34 KB | 0c64bc658446831407b9a69a47dd561f |
| genomic_resource.yaml | 3.51 KB | 4b63f6b7efc20ef15d7430602465a4df |
| statistics/ |