TF_ChIP-seq_ENCSR819ATC
TF_ChIP-seq ENCSR819ATC [biosample_summary="Homo sapiens GM12878" and target="MYB"]
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| Id: | TF_ChIP-seq/ENCSR819ATC |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR819ATC [biosamplesummary="Homo sapiens GM12878" and target="MYB"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 3 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN794VEM|/analyses/ENCAN794VEM/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF821WKC|/files/ENCFF821WKC/} processed by ChIP-seq ENCODE3 hg19 pipeline has 13216380 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting MYB-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 {ENCFF249XQG|/files/ENCFF249XQG/} processed by ChIP-seq ENCODE3 hg19 pipeline has 17645171 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting MYB-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 {ENCFF821WKC|/files/ENCFF821WKC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.88. 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 {ENCFF821WKC|/files/ENCFF821WKC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.79. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF890XSD|/files/ENCFF890XSD/}, {ENCFF157SEX|/files/ENCFF157SEX/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.30 and a self consistency ratio of 2.35. 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 {ENCFF103IOJ|/files/ENCFF103IOJ/}, {ENCFF173YZN|/files/ENCFF173YZN/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.30 and a self consistency ratio of 2.35. 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 {ENCFF348FWJ|/files/ENCFF348FWJ/}, {ENCFF335LXU|/files/ENCFF335LXU/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.32 and a self consistency ratio of 2.54. 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 {ENCFF215YWS|/files/ENCFF215YWS/}, {ENCFF299VKC|/files/ENCFF299VKC/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.32 and a self consistency ratio of 2.54. 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_ENCSR819ATC | float |
TF_ChIP-seq_ENCSR819ATC |
TF_ChIP-seq ENCSR819ATC [biosample_summary="Homo sapiens GM12878" and target="MYB"]
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[4.46, 250] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF215YWS.bed.gz | 67.0 KB | 8ed3e2fdd452d687250b30c3559dcba6 |
| ENCFF215YWS.bed.gz.dvc | 99.0 B | fbc77deb1a455ad966e02853e15f292c |
| ENCFF215YWS.tabix.bed.gz | 48.17 KB | 0ba250e9949e54036691e91d0fd6a22f |
| ENCFF215YWS.tabix.bed.gz.dvc | 105.0 B | f6e5f779546a4771be1fc151bd28ab09 |
| ENCFF215YWS.tabix.bed.gz.tbi | 36.07 KB | e92369d8376267855178bca6c0e5223d |
| ENCFF215YWS.tabix.bed.gz.tbi.dvc | 109.0 B | 09e187f38529097bb0a04ca269001174 |
| genomic_resource.yaml | 5.89 KB | 436ec662274549502bb362aa23fe1525 |
| genomic_resource_original.yaml | 5.79 KB | 1bb62745f8d1b55973a5199bc39e88c1 |
| statistics/ |