TF_ChIP-seq_ENCSR000EFS
TF_ChIP-seq ENCSR000EFS [biosample_summary="Homo sapiens K562" and target="JUN"]
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| Id: | TF_ChIP-seq/ENCSR000EFS |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000EFS [biosamplesummary="Homo sapiens K562" and target="JUN"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN008PXQ|/analyses/ENCAN008PXQ/} has in progress subobject document {58f57096-78a1-42cd-908c-c3729fdc678c|/documents/58f57096-78a1-42cd-908c-c3729fdc678c/} audit_internal_action: Released analysis {ENCAN008PXQ|/analyses/ENCAN008PXQ/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF440KHN|/files/ENCFF440KHN/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 10606238 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting JUN-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 {ENCFF440KHN|/files/ENCFF440KHN/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF440KHN|/files/ENCFF440KHN/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.53. 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 {ENCFF014HSG|/files/ENCFF014HSG/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF014HSG|/files/ENCFF014HSG/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.35. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF190CGV|/files/ENCFF190CGV/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 1.18 and a self consistency ratio of 2.39. 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_ENCSR000EFS | float |
TF_ChIP-seq_ENCSR000EFS |
TF_ChIP-seq ENCSR000EFS [biosample_summary="Homo sapiens K562" and target="JUN"]
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[5.06, 364] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF190CGV.bed.gz | 376.11 KB | 0b84679d4db1348b9e27da599dccbe9a |
| ENCFF190CGV.bed.gz.dvc | 100.0 B | f59ed92d6511e3752119d1e1cf1b5024 |
| ENCFF190CGV.tabix.bed.gz | 256.94 KB | 0837fd66dff4384b2fe18dedb092630b |
| ENCFF190CGV.tabix.bed.gz.dvc | 106.0 B | 497127e27b4c5a2b62a67d20c0be000a |
| ENCFF190CGV.tabix.bed.gz.tbi | 140.31 KB | 1429c64d05026b801ba3485745cfcbf4 |
| ENCFF190CGV.tabix.bed.gz.tbi.dvc | 110.0 B | f4dd7a1510a08cfa4d80080367af6c29 |
| genomic_resource.yaml | 5.22 KB | 12d0dd73af83de6cc5baef8ecc67cfb8 |
| genomic_resource_original.yaml | 5.13 KB | 870d82e44b3b462369da286d15d0c766 |
| statistics/ |