TF_ChIP-seq_ENCSR215XSZ
TF_ChIP-seq ENCSR215XSZ [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens ZMAT5" and target="ZMAT5"]
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| Id: | TF_ChIP-seq/ENCSR215XSZ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR215XSZ [biosamplesummary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens ZMAT5" and target="ZMAT5"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: genetically modified (insertion) using CRISPR targeting H. sapiens ZMAT5 output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN547BBI|/analyses/ENCAN547BBI/} has in progress subobject document {2cb75ed8-590c-4138-a41a-6a7004bd1fa7|/documents/2cb75ed8-590c-4138-a41a-6a7004bd1fa7/} audit_internal_action: Released analysis {ENCAN547BBI|/analyses/ENCAN547BBI/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF327ITV|/files/ENCFF327ITV/} processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline has 18877587 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting ZMAT5-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 {ENCFF015ZOD|/files/ENCFF015ZOD/} processed by ChIP-seq ENCODE4 v1.5.0 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 {ENCFF015ZOD|/files/ENCFF015ZOD/} processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline was generated from a library with PBC2 value of 9.56. 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 {ENCFF327ITV|/files/ENCFF327ITV/} processed by ChIP-seq ENCODE4 v1.5.0 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 {ENCFF327ITV|/files/ENCFF327ITV/} processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline was generated from a library with PBC2 value of 9.31. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF896EHN|/files/ENCFF896EHN/} processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline have a rescue ratio of 1.66 and a self consistency ratio of 3.90. 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 {ENCFF128CWY|/files/ENCFF128CWY/} processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline have a rescue ratio of 1.66 and a self consistency ratio of 3.90. 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_ENCSR215XSZ | float |
TF_ChIP-seq_ENCSR215XSZ |
TF_ChIP-seq ENCSR215XSZ [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens ZMAT5" and target="ZMAT5"]
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[7.21, 323] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF896EHN.bed.gz | 16.18 KB | c919c3856ea5cb67e66a5cbcad93cf8c |
| ENCFF896EHN.bed.gz.dvc | 99.0 B | 8e99acf620b2b357eb60c0233de32375 |
| ENCFF896EHN.tabix.bed.gz | 11.66 KB | baeeb2f01f9579647085356f4ff0d43d |
| ENCFF896EHN.tabix.bed.gz.dvc | 105.0 B | 630d4ba05cbd03fc067da60d2c187284 |
| ENCFF896EHN.tabix.bed.gz.tbi | 11.16 KB | 4bc20656c35d5a662ba51d86f077cb00 |
| ENCFF896EHN.tabix.bed.gz.tbi.dvc | 109.0 B | b0835cb200c4901802d387e9ca5d9c2d |
| genomic_resource.yaml | 5.97 KB | 763f3bdd5b7ec2bd5148813a25ce50f3 |
| genomic_resource_original.yaml | 5.81 KB | 98833317a2db9388e9455cb42ecbc0ce |
| statistics/ |