TF_ChIP-seq_ENCSR000BGL
TF_ChIP-seq ENCSR000BGL [biosample_summary="Homo sapiens HepG2" and target="SIN3A"]
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| Id: | TF_ChIP-seq/ENCSR000BGL |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000BGL [biosamplesummary="Homo sapiens HepG2" and target="SIN3A"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN095ITQ|/analyses/ENCAN095ITQ/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_internal_action: File {ENCFF635YMI|/files/ENCFF635YMI/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_warning: Processed alignments file {ENCFF281FRR|/files/ENCFF281FRR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 10369971 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting SIN3A-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 {ENCFF281FRR|/files/ENCFF281FRR/} 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 {ENCFF281FRR|/files/ENCFF281FRR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.09. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF222NHS|/files/ENCFF222NHS/}, {ENCFF635YMI|/files/ENCFF635YMI/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.32 and a self consistency ratio of 6.66. 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 {ENCFF735FHH|/files/ENCFF735FHH/}, {ENCFF025EZP|/files/ENCFF025EZP/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.32 and a self consistency ratio of 6.66. 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: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BGL | float |
TF_ChIP-seq_ENCSR000BGL |
TF_ChIP-seq ENCSR000BGL [biosample_summary="Homo sapiens HepG2" and target="SIN3A"]
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[5.78, 363] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF635YMI.bed.gz | 402.55 KB | cc228b7f113019a06503b2dc60844057 |
| ENCFF635YMI.bed.gz.dvc | 100.0 B | 3d624578dfe16ebfd5c318396b02fcc7 |
| ENCFF635YMI.tabix.bed.gz | 319.26 KB | b081613444aff9c10d83c8bd29064e60 |
| ENCFF635YMI.tabix.bed.gz.dvc | 106.0 B | 1fbf0a193964d2eee3273c35d408da54 |
| ENCFF635YMI.tabix.bed.gz.tbi | 111.46 KB | e9b1dc53b2faa1bf469cca4d93768eed |
| ENCFF635YMI.tabix.bed.gz.tbi.dvc | 110.0 B | 19401038a8e896e4501ab503f5ab64c2 |
| genomic_resource.yaml | 4.46 KB | 07e2f95e4a48fcf00e75b49f85e881e5 |
| genomic_resource_original.yaml | 4.37 KB | 78dc42eb1c5496c28fcdcc12f1cd1cc1 |
| statistics/ |