TF_ChIP-seq_ENCSR000BTP
TF_ChIP-seq ENCSR000BTP [biosample_summary="Homo sapiens MCF-7" and target="HDAC2"]
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| Id: | TF_ChIP-seq/ENCSR000BTP |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000BTP [biosamplesummary="Homo sapiens MCF-7" and target="HDAC2"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN687VIJ|/analyses/ENCAN687VIJ/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF921VFP|/files/ENCFF921VFP/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 17516642 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting HDAC2-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 {ENCFF921VFP|/files/ENCFF921VFP/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF921VFP|/files/ENCFF921VFP/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 5.95. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF661VXV|/files/ENCFF661VXV/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 1.42 and a self consistency ratio of 2.07. 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_ENCSR000BTP | float |
TF_ChIP-seq_ENCSR000BTP |
TF_ChIP-seq ENCSR000BTP [biosample_summary="Homo sapiens MCF-7" and target="HDAC2"]
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[5.7, 385] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF661VXV.bed.gz | 371.43 KB | 2848f752f422115719ad86ccb4bdacce |
| ENCFF661VXV.bed.gz.dvc | 100.0 B | cc5677da5266cb1050d5743c0c45401e |
| ENCFF661VXV.tabix.bed.gz | 263.2 KB | 386d59721827b84f74b499cfae705acb |
| ENCFF661VXV.tabix.bed.gz.dvc | 106.0 B | dd0235e0bf7503a1f7ed695f1a603384 |
| ENCFF661VXV.tabix.bed.gz.tbi | 135.74 KB | 4cc3cbcb8c1e2b174ed5ed861e8a2734 |
| ENCFF661VXV.tabix.bed.gz.tbi.dvc | 110.0 B | 91ea33f7c323c50af344e528a221d207 |
| genomic_resource.yaml | 3.69 KB | bf5407cd6c0b97585162062b69b4eccc |
| genomic_resource_original.yaml | 3.6 KB | 40705d0b7119e948146129a92c495cb1 |
| statistics/ |