Resource
| Id | TF_ChIP-seq/ENCSR000BHO |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BHO [biosample_summary="Homo sapiens H1" and target="TAF1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN158UFH|/analyses/ENCAN158UFH/} has in progress subobject document {bb933163-2caf-490d-ac8f-5ad7030b0d41|/documents/bb933163-2caf-490d-ac8f-5ad7030b0d41/} audit_internal_action: Released analysis {ENCAN158UFH|/analyses/ENCAN158UFH/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF702DIC|/files/ENCFF702DIC/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 11981013 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 {ENCFF426USV|/files/ENCFF426USV/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 11236939 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 {ENCFF426USV|/files/ENCFF426USV/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.90. 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 {ENCFF426USV|/files/ENCFF426USV/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.54. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BHO | float |
TF_ChIP-seq_ENCSR000BHO |
TF_ChIP-seq ENCSR000BHO [biosample_summary="Homo sapiens H1" and target="TAF1"]
|
 |
[4.1, 486] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10823007 | 0.34% | 33169 |
| chr1 | 1110269 | 0.45% | 3416 |
| chr2 | 745523 | 0.31% | 2287 |
| chr3 | 604639 | 0.30% | 1837 |
| chr4 | 403798 | 0.21% | 1209 |
| chr5 | 506690 | 0.28% | 1546 |
| chr6 | 657256 | 0.38% | 2010 |
| chr7 | 520496 | 0.33% | 1578 |
| chr8 | 387006 | 0.27% | 1198 |
| chr9 | 427803 | 0.31% | 1301 |
| chr10 | 445242 | 0.33% | 1407 |
| chr11 | 584479 | 0.43% | 1752 |
| chr12 | 579666 | 0.43% | 1775 |
| chr13 | 229438 | 0.20% | 717 |
| chr14 | 368146 | 0.34% | 1168 |
| chr15 | 343660 | 0.34% | 1054 |
| chr16 | 433593 | 0.48% | 1335 |
| chr17 | 603677 | 0.73% | 1860 |
| chr18 | 182700 | 0.23% | 564 |
| chr19 | 752619 | 1.28% | 2321 |
| chr20 | 288655 | 0.45% | 870 |
| chr21 | 98404 | 0.21% | 286 |
| chr22 | 245245 | 0.48% | 762 |
| chrX | 295187 | 0.19% | 895 |
| chrY | 8816 | 0.02% | 21 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 33169 | 1 | 1714 | 326.3 | 301 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF886BPR.bed.gz | 475.46 KB | 65ef109b2d64a505af73089d36711865 |
| ENCFF886BPR.tabix.bed.gz | 378.71 KB | 541bf68793fff90b40f8ed931b4f150f |
| ENCFF886BPR.tabix.bed.gz.tbi | 145.29 KB | 75eb6e4ea031252c39b3c2847ce593bd |
| genomic_resource.yaml | 3.86 KB | 2c2d138d90883329ba93c2e8538e32ee |
| statistics/ |