TF_ChIP-seq_ENCSR862VDD
TF_ChIP-seq ENCSR862VDD [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens ZIK1" and target="ZIK1"]
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| Id: | TF_ChIP-seq/ENCSR862VDD |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR862VDD [biosamplesummary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens ZIK1" and target="ZIK1"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: genetically modified (insertion) using CRISPR targeting H. sapiens ZIK1 output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN041PAD|/analyses/ENCAN041PAD/} has in progress subobject document {a90e4c26-3524-4b38-a556-f8fdaec014ca|/documents/a90e4c26-3524-4b38-a556-f8fdaec014ca/} audit_internal_action: Released analysis {ENCAN041PAD|/analyses/ENCAN041PAD/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF982WBW|/files/ENCFF982WBW/} processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline has 18823739 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting ZIK1-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 {ENCFF895QVN|/files/ENCFF895QVN/} processed by ChIP-seq ENCODE4 v1.5.0 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 {ENCFF895QVN|/files/ENCFF895QVN/} processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline was generated from a library with PBC2 value of 9.43. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF009LDQ|/files/ENCFF009LDQ/} processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline have a rescue ratio of 1.13 and a self consistency ratio of 2.40. 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 {ENCFF031XIP|/files/ENCFF031XIP/} processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline have a rescue ratio of 1.13 and a self consistency ratio of 2.40. 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_ENCSR862VDD | float |
TF_ChIP-seq_ENCSR862VDD |
TF_ChIP-seq ENCSR862VDD [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens ZIK1" and target="ZIK1"]
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[7.52, 455] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF009LDQ.bed.gz | 187.39 KB | fd90002e9513ae257b2e2e15c6e8b56e |
| ENCFF009LDQ.bed.gz.dvc | 100.0 B | 5bdf7e2f56ccaeb12a56094e3d553bb1 |
| ENCFF009LDQ.tabix.bed.gz | 153.67 KB | d596389f2b2e50a3e65327e21eaab85d |
| ENCFF009LDQ.tabix.bed.gz.dvc | 106.0 B | 818fafea42a2cb3787661c41f0ea9fdf |
| ENCFF009LDQ.tabix.bed.gz.tbi | 72.39 KB | f2c86a69c1fb6008546f569fc8558e25 |
| ENCFF009LDQ.tabix.bed.gz.tbi.dvc | 109.0 B | 6adaf1b90ef286341819fcd384bbc166 |
| genomic_resource.yaml | 4.69 KB | 4530614a0da9708d0f64fc9cf1e957de |
| genomic_resource_original.yaml | 4.53 KB | d28b037d9533d6abfad50a3672a63d57 |
| statistics/ |