TF_ChIP-seq_ENCSR000BUQ
TF_ChIP-seq ENCSR000BUQ [biosample_summary="Homo sapiens SK-N-SH" and target="TEAD4"]
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| Id: | TF_ChIP-seq/ENCSR000BUQ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000BUQ [biosamplesummary="Homo sapiens SK-N-SH" and target="TEAD4"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN393ETY|/analyses/ENCAN393ETY/} has in progress subobject document {1b3ae27e-e0d3-4cff-9881-1776da6f36e1|/documents/1b3ae27e-e0d3-4cff-9881-1776da6f36e1/} audit_internal_action: Released analysis {ENCAN393ETY|/analyses/ENCAN393ETY/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF031WOZ|/files/ENCFF031WOZ/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline has 8540741 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting TEAD4-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 {ENCFF031WOZ|/files/ENCFF031WOZ/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF031WOZ|/files/ENCFF031WOZ/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC2 value of 7.81. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF463DWW|/files/ENCFF463DWW/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of 1.14 and a self consistency ratio of 2.31. 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 {ENCFF754TJT|/files/ENCFF754TJT/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of 1.14 and a self consistency ratio of 2.31. 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_ENCSR000BUQ | float |
TF_ChIP-seq_ENCSR000BUQ |
TF_ChIP-seq ENCSR000BUQ [biosample_summary="Homo sapiens SK-N-SH" and target="TEAD4"]
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[4.52, 330] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF463DWW.bed.gz | 426.77 KB | ce6a37a302ed25ed870389fec41947cf |
| ENCFF463DWW.bed.gz.dvc | 100.0 B | c5c428aa3220a9edbeeb06b1bca6bca8 |
| ENCFF463DWW.tabix.bed.gz | 307.09 KB | 225d118aca46d811a39dd6188e066155 |
| ENCFF463DWW.tabix.bed.gz.dvc | 106.0 B | 11f7a225ba80a9c7a4ff7fe5cd330634 |
| ENCFF463DWW.tabix.bed.gz.tbi | 148.95 KB | 465c80d42c4bb97abe8343a113e17109 |
| ENCFF463DWW.tabix.bed.gz.tbi.dvc | 110.0 B | bb6f8e83c3758ba4c0b3ccca7841c221 |
| genomic_resource.yaml | 4.47 KB | 12b381559ab5040388bcb6aaf1383182 |
| genomic_resource_original.yaml | 4.37 KB | bf782bc2d448939f3074a68ca8d43db7 |
| statistics/ |