TF_ChIP-seq_ENCSR459FTB
TF_ChIP-seq ENCSR459FTB [biosample_summary="Homo sapiens GM12878" and target="UBTF"]
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| Id: | TF_ChIP-seq/ENCSR459FTB |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR459FTB [biosamplesummary="Homo sapiens GM12878" and target="UBTF"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN214FDK|/analyses/ENCAN214FDK/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF370YOR|/files/ENCFF370YOR/} processed by ChIP-seq ENCODE3 hg19 pipeline has 19400374 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting UBTF-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 {ENCFF688XDE|/files/ENCFF688XDE/} processed by ChIP-seq ENCODE3 hg19 pipeline has 13021124 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting UBTF-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 {ENCFF688XDE|/files/ENCFF688XDE/} 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 {ENCFF688XDE|/files/ENCFF688XDE/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.71. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF754GFB|/files/ENCFF754GFB/}, {ENCFF802EUE|/files/ENCFF802EUE/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.46 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 {ENCFF930SKY|/files/ENCFF930SKY/}, {ENCFF846HFA|/files/ENCFF846HFA/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.57 and a self consistency ratio of 2.66. 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 {ENCFF499CTR|/files/ENCFF499CTR/}, {ENCFF745TNJ|/files/ENCFF745TNJ/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.46 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 {ENCFF298UPI|/files/ENCFF298UPI/}, {ENCFF791WCX|/files/ENCFF791WCX/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.57 and a self consistency ratio of 2.66. 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_ENCSR459FTB | float |
TF_ChIP-seq_ENCSR459FTB |
TF_ChIP-seq ENCSR459FTB [biosample_summary="Homo sapiens GM12878" and target="UBTF"]
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[4.52, 301] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF298UPI.bed.gz | 27.86 KB | c82f947c982c796763283fc21f4ad097 |
| ENCFF298UPI.bed.gz.dvc | 99.0 B | 36d692c0a355a4f94071ba26a48e112c |
| ENCFF298UPI.tabix.bed.gz | 18.79 KB | c34fa56ee0c69be693c9321704868bbe |
| ENCFF298UPI.tabix.bed.gz.dvc | 105.0 B | 02140c52cb60a943b8013421ae3cef0f |
| ENCFF298UPI.tabix.bed.gz.tbi | 18.45 KB | 92d0ccc08e571477da835934bf320656 |
| ENCFF298UPI.tabix.bed.gz.tbi.dvc | 109.0 B | 250039e22cc7dc61f62e6f574da9052a |
| genomic_resource.yaml | 5.89 KB | 5f13558b4c4df4722b74d6ed07197497 |
| genomic_resource_original.yaml | 5.79 KB | 80a8628c2e7671e8b71338c610917aa4 |
| statistics/ |