TF_ChIP-seq_ENCSR000BGM
TF_ChIP-seq ENCSR000BGM [biosample_summary="Homo sapiens HepG2" and target="USF1"]
×
| Id: | TF_ChIP-seq/ENCSR000BGM |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000BGM [biosamplesummary="Homo sapiens HepG2" and target="USF1"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: File {ENCFF914IFQ|/files/ENCFF914IFQ/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_internal_action: Archived analysis {ENCAN117NQJ|/analyses/ENCAN117NQJ/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF582CJF|/files/ENCFF582CJF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 12638677 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting USF1-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 {ENCFF582CJF|/files/ENCFF582CJF/} processed by ChIP-seq ENCODE3 GRCh38 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 {ENCFF582CJF|/files/ENCFF582CJF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.33. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF498RHX|/files/ENCFF498RHX/}, {ENCFF586WRZ|/files/ENCFF586WRZ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.25 and a self consistency ratio of 2.35. 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 {ENCFF895AOF|/files/ENCFF895AOF/}, {ENCFF914IFQ|/files/ENCFF914IFQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.25 and a self consistency ratio of 2.35. 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: |
|
| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BGM | float |
TF_ChIP-seq_ENCSR000BGM |
TF_ChIP-seq ENCSR000BGM [biosample_summary="Homo sapiens HepG2" and target="USF1"]
|
|
[4.44, 414] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF914IFQ.bed.gz | 386.59 KB | 17a74daeb420617d9eecadc51715cc37 |
| ENCFF914IFQ.bed.gz.dvc | 100.0 B | 77570fad44c57d6e1233d038451041fc |
| ENCFF914IFQ.tabix.bed.gz | 281.22 KB | 7e8b80626be0fcba1424e4383e2c331e |
| ENCFF914IFQ.tabix.bed.gz.dvc | 106.0 B | 83c5725f23fc15f72897459ffc066a9c |
| ENCFF914IFQ.tabix.bed.gz.tbi | 160.57 KB | 5a8691506357606d8805fc63185e8bd2 |
| ENCFF914IFQ.tabix.bed.gz.tbi.dvc | 110.0 B | 14acdf52c748e6c8b3b1c7382497735c |
| genomic_resource.yaml | 4.46 KB | 95701542de26fa74ff4d56b29633b8bd |
| genomic_resource_original.yaml | 4.37 KB | b481866c6fea7072c9616c7bc628e07c |
| statistics/ |