TF_ChIP-seq_ENCSR213QOZ
TF_ChIP-seq ENCSR213QOZ [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens SMAD1" and target="SMAD1"]
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| Id: | TF_ChIP-seq/ENCSR213QOZ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR213QOZ [biosamplesummary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens SMAD1" and target="SMAD1"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: genetically modified (insertion) using CRISPR targeting H. sapiens SMAD1 output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN348NIS|/analyses/ENCAN348NIS/} has replaced subobject file {3616f164-259d-4a0c-b830-d90e3a47f53e|/files/3616f164-259d-4a0c-b830-d90e3a47f53e/} audit_internal_action: Released analysis {ENCAN348NIS|/analyses/ENCAN348NIS/} has replaced subobject file {54529bbd-4fac-4e0b-8983-e153b076c73e|/files/54529bbd-4fac-4e0b-8983-e153b076c73e/} audit_internal_action: Released analysis {ENCAN348NIS|/analyses/ENCAN348NIS/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_internal_action: Released analysis {ENCAN348NIS|/analyses/ENCAN348NIS/} has replaced subobject file {09e03f5d-d3eb-415e-b182-f269bb0ec6ba|/files/09e03f5d-d3eb-415e-b182-f269bb0ec6ba/} audit_internal_action: Released analysis {ENCAN348NIS|/analyses/ENCAN348NIS/} has in progress subobject document {0837f515-a130-40f8-be9d-0cc47dd8a146|/documents/0837f515-a130-40f8-be9d-0cc47dd8a146/} audit_internal_action: Released analysis {ENCAN348NIS|/analyses/ENCAN348NIS/} has replaced subobject file {b402214c-bf99-4ce8-a837-13f1adb9e7fd|/files/b402214c-bf99-4ce8-a837-13f1adb9e7fd/} audit_warning: Processed alignments file {ENCFF968XFW|/files/ENCFF968XFW/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline has 19734125 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting SMAD1-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 {ENCFF968XFW|/files/ENCFF968XFW/} processed by ChIP-seq ENCODE4 v1.4.0 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 {ENCFF968XFW|/files/ENCFF968XFW/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC2 value of 8.90. 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 {ENCFF781SQE|/files/ENCFF781SQE/} processed by ChIP-seq ENCODE4 v1.4.0 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 {ENCFF781SQE|/files/ENCFF781SQE/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC2 value of 9.72. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF243JXS|/files/ENCFF243JXS/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of 1.94 and a self consistency ratio of 5.36. 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 {ENCFF892OZT|/files/ENCFF892OZT/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of 1.94 and a self consistency ratio of 5.36. 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_ENCSR213QOZ | float |
TF_ChIP-seq_ENCSR213QOZ |
TF_ChIP-seq ENCSR213QOZ [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens SMAD1" and target="SMAD1"]
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[9.11, 239] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF243JXS.bed.gz | 198.43 KB | c415c1de93fced4c4f5f767ccdb85b57 |
| ENCFF243JXS.bed.gz.dvc | 100.0 B | e853794ce9f59a01c7aa32bcfb152116 |
| ENCFF243JXS.tabix.bed.gz | 160.88 KB | e1a6a12c70aade111cba75c0e71e29cb |
| ENCFF243JXS.tabix.bed.gz.dvc | 106.0 B | 384cfe0d09c061a1b9b5eb336fccc0e6 |
| ENCFF243JXS.tabix.bed.gz.tbi | 72.0 KB | f351bf15a9a5058e2ebcc162cae6dbe0 |
| ENCFF243JXS.tabix.bed.gz.tbi.dvc | 109.0 B | 3021701e96733d58115718f8fe66b0e5 |
| genomic_resource.yaml | 6.77 KB | aa4b15ce89e7c917b2e2608eb23c016b |
| genomic_resource_original.yaml | 6.61 KB | a4a4f62a40e854c475a4fd19c248bcf5 |
| statistics/ |