TF_ChIP-seq_ENCSR422ZAO
TF_ChIP-seq ENCSR422ZAO [biosample_summary="Homo sapiens SK-N-SH" and target="IRF3"]
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| Id: | TF_ChIP-seq/ENCSR422ZAO |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR422ZAO [biosamplesummary="Homo sapiens SK-N-SH" and target="IRF3"] |
| Description: |
status: released biological_replicates: Rep 2, Rep 3 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN418DAS|/analyses/ENCAN418DAS/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF247DGL|/files/ENCFF247DGL/} processed by ChIP-seq ENCODE3 hg19 pipeline has 17877206 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting IRF3-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: Processed alignments file {ENCFF588CRQ|/files/ENCFF588CRQ/} processed by ChIP-seq ENCODE3 hg19 pipeline has 16210089 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting IRF3-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 {ENCFF247DGL|/files/ENCFF247DGL/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF247DGL|/files/ENCFF247DGL/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 9.13. 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 {ENCFF588CRQ|/files/ENCFF588CRQ/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF588CRQ|/files/ENCFF588CRQ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.26. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF503SZB|/files/ENCFF503SZB/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.38 and a self consistency ratio of 4.53. 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 {ENCFF036ILD|/files/ENCFF036ILD/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.38 and a self consistency ratio of 4.53. 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_ENCSR422ZAO | float |
TF_ChIP-seq_ENCSR422ZAO |
TF_ChIP-seq ENCSR422ZAO [biosample_summary="Homo sapiens SK-N-SH" and target="IRF3"]
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[9.88, 257] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF503SZB.bed.gz | 18.48 KB | 2aea4dec6d18664385af8d5c9fd590ef |
| ENCFF503SZB.bed.gz.dvc | 99.0 B | c924a9eef57b0a5c0d1b862399adeb42 |
| ENCFF503SZB.tabix.bed.gz | 12.69 KB | a68a0d76dd01959fca94cf1e9f136997 |
| ENCFF503SZB.tabix.bed.gz.dvc | 105.0 B | 540677ea089c66efb7efc23fdfd0109f |
| ENCFF503SZB.tabix.bed.gz.tbi | 15.16 KB | 1d677b4a005f3624be70c9e57bc3175e |
| ENCFF503SZB.tabix.bed.gz.tbi.dvc | 109.0 B | a27af08afa65370f51d51e84431d0ffc |
| genomic_resource.yaml | 5.99 KB | 63bb3ca5e0fa01a86b9dd430c966d1db |
| genomic_resource_original.yaml | 5.89 KB | 220e29a5ec6b9ced3a0acc6098ef8349 |
| statistics/ |