TF_ChIP-seq_ENCSR000BKO
TF_ChIP-seq ENCSR000BKO [biosample_summary="Homo sapiens K562" and target="SP1"]
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| Id: | TF_ChIP-seq/ENCSR000BKO |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000BKO [biosamplesummary="Homo sapiens K562" and target="SP1"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN454PMN|/analyses/ENCAN454PMN/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_internal_action: Released analysis {ENCAN454PMN|/analyses/ENCAN454PMN/} has in progress subobject document {ce94a34f-4090-49bc-87fb-242213021ece|/documents/ce94a34f-4090-49bc-87fb-242213021ece/} audit_warning: Processed alignments file {ENCFF617EYG|/files/ENCFF617EYG/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 13657348 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting SP1-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 {ENCFF716PNY|/files/ENCFF716PNY/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 17621347 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting SP1-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 {ENCFF617EYG|/files/ENCFF617EYG/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.90. 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 {ENCFF617EYG|/files/ENCFF617EYG/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.41. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF171NEU|/files/ENCFF171NEU/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 1.16 and a self consistency ratio of 2.61. 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_ENCSR000BKO | float |
TF_ChIP-seq_ENCSR000BKO |
TF_ChIP-seq ENCSR000BKO [biosample_summary="Homo sapiens K562" and target="SP1"]
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[4.71, 447] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF171NEU.bed.gz | 139.55 KB | ed96812047e32cf031bf7a494bbcfc54 |
| ENCFF171NEU.bed.gz.dvc | 100.0 B | 59bac722f15dfa7132c29fbc1ab2fc44 |
| ENCFF171NEU.tabix.bed.gz | 96.64 KB | 995bbf5aba28e9ee9db0a52a157eaf2b |
| ENCFF171NEU.tabix.bed.gz.dvc | 105.0 B | 613fec9d13da5335b423511ae2f7206a |
| ENCFF171NEU.tabix.bed.gz.tbi | 64.13 KB | e94475cadbf6c2c51448314f6262cee6 |
| ENCFF171NEU.tabix.bed.gz.tbi.dvc | 109.0 B | 615434a7c08ac5257b40fe6633e91625 |
| genomic_resource.yaml | 4.41 KB | 9561abad6b8467106ff91d56d062bf5d |
| genomic_resource_original.yaml | 4.31 KB | 96f7c278fc3608e321aeb9f40d9e1e99 |
| statistics/ |