Resource
| Id | TF_ChIP-seq/ENCSR000BHT |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BHT [biosample_summary="Homo sapiens HeLa-S3" and target="TAF1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN031NQH|/analyses/ENCAN031NQH/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF352NJI|/files/ENCFF352NJI/} processed by ChIP-seq ENCODE3 hg19 pipeline has 8887980 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting TAF1-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 {ENCFF654DIS|/files/ENCFF654DIS/} processed by ChIP-seq ENCODE3 hg19 pipeline has 13702469 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting TAF1-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 {ENCFF654DIS|/files/ENCFF654DIS/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF654DIS|/files/ENCFF654DIS/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.13. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BHT | float |
TF_ChIP-seq_ENCSR000BHT |
TF_ChIP-seq ENCSR000BHT [biosample_summary="Homo sapiens HeLa-S3" and target="TAF1"]
|
 |
[3.87, 381] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5514373 | 0.17% | 20462 |
| chr1 | 555078 | 0.22% | 2074 |
| chr2 | 336590 | 0.14% | 1236 |
| chr3 | 341690 | 0.17% | 1257 |
| chr4 | 158820 | 0.08% | 574 |
| chr5 | 313935 | 0.17% | 1179 |
| chr6 | 330119 | 0.19% | 1231 |
| chr7 | 250754 | 0.16% | 925 |
| chr8 | 221832 | 0.15% | 829 |
| chr9 | 257349 | 0.19% | 943 |
| chr10 | 236853 | 0.18% | 876 |
| chr11 | 315589 | 0.23% | 1180 |
| chr12 | 333045 | 0.25% | 1258 |
| chr13 | 101639 | 0.09% | 356 |
| chr14 | 188996 | 0.18% | 713 |
| chr15 | 218193 | 0.21% | 828 |
| chr16 | 211440 | 0.23% | 758 |
| chr17 | 315340 | 0.38% | 1161 |
| chr18 | 105458 | 0.13% | 407 |
| chr19 | 255295 | 0.44% | 947 |
| chr20 | 150434 | 0.23% | 556 |
| chr21 | 65045 | 0.14% | 245 |
| chr22 | 82755 | 0.16% | 295 |
| chrX | 168124 | 0.11% | 634 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 20462 | 1 | 604 | 269.49 | 330 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF305QDB.bed.gz | 305.12 KB | 212dacefd25c5361bc1b2e5400f36d9c |
| ENCFF305QDB.tabix.bed.gz | 233.55 KB | 05c8d7715382e01e45bb83dcb2dcda96 |
| ENCFF305QDB.tabix.bed.gz.tbi | 105.46 KB | 5692491273f92f5e3c20a445c3e0532b |
| genomic_resource.yaml | 3.64 KB | 9655ddf13d77399173f7544d0db083f0 |
| statistics/ |