TF_ChIP-seq_ENCSR000DKZ
TF_ChIP-seq ENCSR000DKZ [biosample_summary="Homo sapiens GM13976" and target="CTCF"]
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| Id: | TF_ChIP-seq/ENCSR000DKZ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000DKZ [biosamplesummary="Homo sapiens GM13976" and target="CTCF"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: File {ENCFF601MPV|/files/ENCFF601MPV/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_internal_action: Archived analysis {ENCAN117OCD|/analyses/ENCAN117OCD/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF651CKC|/files/ENCFF651CKC/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 6690869 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-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_not_compliant: Processed alignments file {ENCFF271LZR|/files/ENCFF271LZR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 8837336 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-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 {ENCFF271LZR|/files/ENCFF271LZR/} processed by ChIP-seq ENCODE3 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 {ENCFF271LZR|/files/ENCFF271LZR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.43. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF392PKQ|/files/ENCFF392PKQ/}, {ENCFF518WLT|/files/ENCFF518WLT/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.43 and a self consistency ratio of 3.99. 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 {ENCFF601MPV|/files/ENCFF601MPV/}, {ENCFF075DWD|/files/ENCFF075DWD/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.43 and a self consistency ratio of 3.99. 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_ENCSR000DKZ | float |
TF_ChIP-seq_ENCSR000DKZ |
TF_ChIP-seq ENCSR000DKZ [biosample_summary="Homo sapiens GM13976" and target="CTCF"]
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[3.88, 353] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF601MPV.bed.gz | 520.54 KB | 8e23cdf9ffb2f77956cf23464f1d2c16 |
| ENCFF601MPV.bed.gz.dvc | 100.0 B | 97a5da5109d4b8f85e52ca1437c0479c |
| ENCFF601MPV.tabix.bed.gz | 377.98 KB | 56984be5e5afd48d3ae77b49d0b38768 |
| ENCFF601MPV.tabix.bed.gz.dvc | 106.0 B | 405f28befb856d728a6ad5a9d516bf1a |
| ENCFF601MPV.tabix.bed.gz.tbi | 223.89 KB | a97c7adaced7895ec9c663872956d772 |
| ENCFF601MPV.tabix.bed.gz.tbi.dvc | 110.0 B | a68d6db70cc894c547cd8563c44671ef |
| genomic_resource.yaml | 4.97 KB | 4ac7c70a8a820f227e3f959781a00091 |
| genomic_resource_original.yaml | 4.88 KB | fb9bf99338f1aa561a62c39e98bf4c1e |
| statistics/ |