TF_ChIP-seq_ENCSR524BUE
TF_ChIP-seq ENCSR524BUE [biosample_summary="Homo sapiens K562" and target="RAD51"]
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| Id: | TF_ChIP-seq/ENCSR524BUE |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR524BUE [biosamplesummary="Homo sapiens K562" and target="RAD51"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN281UKB|/analyses/ENCAN281UKB/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF650WIA|/files/ENCFF650WIA/} processed by ChIP-seq ENCODE3 hg19 pipeline has 18409712 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting RAD51-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 {ENCFF254KBN|/files/ENCFF254KBN/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF254KBN|/files/ENCFF254KBN/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.43. 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 {ENCFF650WIA|/files/ENCFF650WIA/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.81. 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 {ENCFF650WIA|/files/ENCFF650WIA/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 4.98. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF096XMD|/files/ENCFF096XMD/}, {ENCFF924XJK|/files/ENCFF924XJK/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.57 and a self consistency ratio of 2.22. 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 {ENCFF973SKX|/files/ENCFF973SKX/}, {ENCFF311KUF|/files/ENCFF311KUF/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.57 and a self consistency ratio of 2.22. 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_ENCSR524BUE | float |
TF_ChIP-seq_ENCSR524BUE |
TF_ChIP-seq ENCSR524BUE [biosample_summary="Homo sapiens K562" and target="RAD51"]
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[30.6, 1.4e+04] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF096XMD.bed.gz | 276.07 KB | 59332e8ca90fc4507468b673efd55907 |
| ENCFF096XMD.bed.gz.dvc | 100.0 B | 9f617f93a004010ecbb9723e2e0e9eef |
| ENCFF096XMD.tabix.bed.gz | 218.17 KB | 928ad72fd0a8edece75b3ad25f5e2d43 |
| ENCFF096XMD.tabix.bed.gz.dvc | 106.0 B | f529c9dfc6880b296eee09ccfca2279a |
| ENCFF096XMD.tabix.bed.gz.tbi | 129.0 KB | 50768ee21941ed9610b1d11d6827383f |
| ENCFF096XMD.tabix.bed.gz.tbi.dvc | 110.0 B | 6f6195bd8b233cf8ff4de719cd7cf304 |
| genomic_resource.yaml | 5.56 KB | baab6dbc714b556925b252ccb6b3b7e0 |
| genomic_resource_original.yaml | 5.47 KB | 9022e3f05db491682197cda5b183c23d |
| statistics/ |