TF_ChIP-seq_ENCSR000AKB
TF_ChIP-seq ENCSR000AKB [biosample_summary="Homo sapiens GM12878" and target="CTCF"]
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| Id: | TF_ChIP-seq/ENCSR000AKB |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000AKB [biosamplesummary="Homo sapiens GM12878" and target="CTCF"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN637WKE|/analyses/ENCAN637WKE/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF389RQC|/files/ENCFF389RQC/} processed by ChIP-seq ENCODE3 hg19 pipeline has 6744960 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: Processed alignments file {ENCFF343LTM|/files/ENCFF343LTM/} processed by ChIP-seq ENCODE3 hg19 pipeline has 14330073 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 {ENCFF389RQC|/files/ENCFF389RQC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF389RQC|/files/ENCFF389RQC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.76. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000AKB | float |
TF_ChIP-seq_ENCSR000AKB |
TF_ChIP-seq ENCSR000AKB [biosample_summary="Homo sapiens GM12878" and target="CTCF"]
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[3.9, 486] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF833FTF.bed.gz | 640.42 KB | 265cfe705263baae508111a4114aab61 |
| ENCFF833FTF.bed.gz.dvc | 100.0 B | ef4b971c2f2f39f0758d0fa27ccc615d |
| ENCFF833FTF.tabix.bed.gz | 492.01 KB | d83a5386e9db03efff7f1a9cdc7aaa08 |
| ENCFF833FTF.tabix.bed.gz.dvc | 106.0 B | e519f17620e02e0134be73f674d8223b |
| ENCFF833FTF.tabix.bed.gz.tbi | 261.6 KB | a37eef71ce99e818d719384c3497f7f0 |
| ENCFF833FTF.tabix.bed.gz.tbi.dvc | 110.0 B | 6688e78195f56ae399075053e8a40551 |
| genomic_resource.yaml | 3.76 KB | bb69064af06f928e02fe4eaf23dfcb1c |
| genomic_resource_original.yaml | 3.66 KB | 07dde804d50bd69fd747cdfb3290e006 |
| statistics/ |