TF_ChIP-seq_ENCSR000BST
TF_ChIP-seq ENCSR000BST [biosample_summary="Homo sapiens MCF-7" and target="GATA3"]
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| Id: | TF_ChIP-seq/ENCSR000BST |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000BST [biosamplesummary="Homo sapiens MCF-7" and target="GATA3"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN399CCN|/analyses/ENCAN399CCN/} has in progress subobject document {5766f25a-70bd-4152-b965-99da255de785|/documents/5766f25a-70bd-4152-b965-99da255de785/} audit_internal_action: Released analysis {ENCAN399CCN|/analyses/ENCAN399CCN/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF944GIS|/files/ENCFF944GIS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 8717931 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting GATA3-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 {ENCFF944GIS|/files/ENCFF944GIS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.83. 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 {ENCFF944GIS|/files/ENCFF944GIS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 5.91. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF565QWY|/files/ENCFF565QWY/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 1.35 and a self consistency ratio of 2.19. 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_ENCSR000BST | float |
TF_ChIP-seq_ENCSR000BST |
TF_ChIP-seq ENCSR000BST [biosample_summary="Homo sapiens MCF-7" and target="GATA3"]
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[4.52, 624] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF565QWY.bed.gz | 774.63 KB | e6836d1f534e7bc0aac03d710684af83 |
| ENCFF565QWY.bed.gz.dvc | 100.0 B | 59ad27ce5ba8bc54007b80e1c9c1a72c |
| ENCFF565QWY.tabix.bed.gz | 570.39 KB | 88876748831b52f57e899311a6bd751f |
| ENCFF565QWY.tabix.bed.gz.dvc | 106.0 B | f21891a7f05029c279e55b060060e145 |
| ENCFF565QWY.tabix.bed.gz.tbi | 268.78 KB | 52824a0811643a4a1348180699c671e5 |
| ENCFF565QWY.tabix.bed.gz.tbi.dvc | 110.0 B | 6a9b4a8fc8fffd71bcb9c2753062dd41 |
| genomic_resource.yaml | 3.92 KB | 3812c2371d74cc39b28b3852564e1a35 |
| genomic_resource_original.yaml | 3.82 KB | 6103b6038149807201cbde4777f9aacc |
| statistics/ |