TF_ChIP-seq_ENCSR000BJX
TF_ChIP-seq ENCSR000BJX [biosample_summary="Homo sapiens HepG2" and target="SP1"]
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| Id: | TF_ChIP-seq/ENCSR000BJX |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000BJX [biosamplesummary="Homo sapiens HepG2" and target="SP1"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN029VQS|/analyses/ENCAN029VQS/} has in progress subobject document {1c22705b-d200-491d-ae6e-fa64bb049aa9|/documents/1c22705b-d200-491d-ae6e-fa64bb049aa9/} audit_internal_action: Released analysis {ENCAN029VQS|/analyses/ENCAN029VQS/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_not_compliant: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF806TIM|/files/ENCFF806TIM/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 11.84 and a self consistency ratio of 86.47. 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: Processed alignments file {ENCFF718SND|/files/ENCFF718SND/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 17793239 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 {ENCFF241ZKB|/files/ENCFF241ZKB/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 12139668 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 {ENCFF241ZKB|/files/ENCFF241ZKB/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF241ZKB|/files/ENCFF241ZKB/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.68. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BJX | float |
TF_ChIP-seq_ENCSR000BJX |
TF_ChIP-seq ENCSR000BJX [biosample_summary="Homo sapiens HepG2" and target="SP1"]
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[4.31, 337] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF806TIM.bed.gz | 441.99 KB | be18a4652cf9648207ba9963b65a34c5 |
| ENCFF806TIM.bed.gz.dvc | 100.0 B | 427d9660e21d7c8c1f85b24c577d6d86 |
| ENCFF806TIM.tabix.bed.gz | 329.92 KB | c6adcb4a0ac94c16035c0feb476c601e |
| ENCFF806TIM.tabix.bed.gz.dvc | 106.0 B | 091fd0614fddfbe475c5f2db7125a841 |
| ENCFF806TIM.tabix.bed.gz.tbi | 157.18 KB | 13ba4fdbd5b0a0640c9b82cd80cc1c36 |
| ENCFF806TIM.tabix.bed.gz.tbi.dvc | 110.0 B | f92cbc4d3d6d110567ef5de77fe08f79 |
| genomic_resource.yaml | 4.42 KB | 6e50527e7fd73de7ef33e089a99d1f82 |
| genomic_resource_original.yaml | 4.33 KB | 5019f49ce9b6fe1789aeacbbc8f63b18 |
| statistics/ |