Resource
| Id | TF_ChIP-seq/ENCSR000BIB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BIB [biosample_summary="Homo sapiens GM12892" and target="TAF1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN614KAE|/analyses/ENCAN614KAE/} has in progress subobject document {485c28c2-4d1e-4e18-87c5-4ea625bcf5e4|/documents/485c28c2-4d1e-4e18-87c5-4ea625bcf5e4/} audit_internal_action: Released analysis {ENCAN614KAE|/analyses/ENCAN614KAE/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF370BIB|/files/ENCFF370BIB/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 14356474 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 {ENCFF063XWS|/files/ENCFF063XWS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 13890074 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 {ENCFF370BIB|/files/ENCFF370BIB/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF370BIB|/files/ENCFF370BIB/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.22. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF594SQR|/files/ENCFF594SQR/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 1.28 and a self consistency ratio of 2.04. 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_ENCSR000BIB | float |
TF_ChIP-seq_ENCSR000BIB |
TF_ChIP-seq ENCSR000BIB [biosample_summary="Homo sapiens GM12892" and target="TAF1"]
|
 |
[4.99, 405] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 3508540 | 0.11% | 13054 |
| chr1 | 360580 | 0.14% | 1345 |
| chr2 | 259550 | 0.11% | 958 |
| chr3 | 188185 | 0.09% | 703 |
| chr4 | 118051 | 0.06% | 451 |
| chr5 | 161569 | 0.09% | 613 |
| chr6 | 212902 | 0.12% | 794 |
| chr7 | 163455 | 0.10% | 604 |
| chr8 | 122902 | 0.08% | 461 |
| chr9 | 136817 | 0.10% | 507 |
| chr10 | 154914 | 0.12% | 574 |
| chr11 | 186113 | 0.14% | 685 |
| chr12 | 188490 | 0.14% | 699 |
| chr13 | 65990 | 0.06% | 245 |
| chr14 | 122650 | 0.11% | 448 |
| chr15 | 116881 | 0.11% | 439 |
| chr16 | 144898 | 0.16% | 540 |
| chr17 | 210479 | 0.25% | 783 |
| chr18 | 51273 | 0.06% | 186 |
| chr19 | 245407 | 0.42% | 919 |
| chr20 | 90210 | 0.14% | 331 |
| chr21 | 35605 | 0.08% | 130 |
| chr22 | 90410 | 0.18% | 339 |
| chrX | 81209 | 0.05% | 300 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 13054 | 1 | 345 | 268.77 | 300 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF594SQR.bed.gz | 208.27 KB | 2d2820288a2a15118d9df787eb7c8436 |
| ENCFF594SQR.tabix.bed.gz | 150.64 KB | 51a5ce3b383ac76e0149d313492b7207 |
| ENCFF594SQR.tabix.bed.gz.tbi | 83.63 KB | 17680f527e056d473958ce2927b9c76f |
| genomic_resource.yaml | 4.42 KB | 50f4c66751135a50123433bcbb4d49ea |
| statistics/ |