TF_ChIP-seq_ENCSR000DMF
TF_ChIP-seq ENCSR000DMF [biosample_summary="Homo sapiens LNCaP clone FGC" and target="CTCF"]
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| Id: | TF_ChIP-seq/ENCSR000DMF |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000DMF [biosamplesummary="Homo sapiens LNCaP clone FGC" and target="CTCF"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN656XQB|/analyses/ENCAN656XQB/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF999JKD|/files/ENCFF999JKD/} processed by ChIP-seq ENCODE3 hg19 pipeline has 8160689 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 {ENCFF776OUN|/files/ENCFF776OUN/} processed by ChIP-seq ENCODE3 hg19 pipeline has 9570833 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 {ENCFF999JKD|/files/ENCFF999JKD/} 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 {ENCFF999JKD|/files/ENCFF999JKD/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.15. 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 {ENCFF776OUN|/files/ENCFF776OUN/} 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 {ENCFF776OUN|/files/ENCFF776OUN/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.60. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000DMF | float |
TF_ChIP-seq_ENCSR000DMF |
TF_ChIP-seq ENCSR000DMF [biosample_summary="Homo sapiens LNCaP clone FGC" and target="CTCF"]
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[3.87, 362] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF988IOQ.bed.gz | 815.99 KB | 229b8bc3f4c57961455ee29ab67d5f55 |
| ENCFF988IOQ.bed.gz.dvc | 100.0 B | 7cd864d9c3a41a74e5f80f3802130278 |
| ENCFF988IOQ.tabix.bed.gz | 614.16 KB | 6403bde629e2dd9572b17d9ebc16fd4c |
| ENCFF988IOQ.tabix.bed.gz.dvc | 106.0 B | 18702268a4d32a44400b844259f8fdb7 |
| ENCFF988IOQ.tabix.bed.gz.tbi | 331.97 KB | 75f35156295ab1fc6572286483c2cba3 |
| ENCFF988IOQ.tabix.bed.gz.tbi.dvc | 110.0 B | d137dd3c577c323ed3aafdb171ff3cda |
| genomic_resource.yaml | 4.97 KB | 7264e331516c59f27be9ff4a075a0279 |
| genomic_resource_original.yaml | 4.86 KB | 9ede0a9670aebabe8473f34082120628 |
| statistics/ |