TF_ChIP-seq_ENCSR000BVG
TF_ChIP-seq ENCSR000BVG [biosample_summary="Homo sapiens SK-N-SH" and target="RXRA"]
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| Id: | TF_ChIP-seq/ENCSR000BVG |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000BVG [biosamplesummary="Homo sapiens SK-N-SH" and target="RXRA"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN109BDR|/analyses/ENCAN109BDR/} has in progress subobject document {8195619e-28c8-4b2d-bea8-9a56311a19d8|/documents/8195619e-28c8-4b2d-bea8-9a56311a19d8/} audit_internal_action: Released analysis {ENCAN109BDR|/analyses/ENCAN109BDR/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF521HYH|/files/ENCFF521HYH/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline has 18418551 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting RXRA-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 {ENCFF521HYH|/files/ENCFF521HYH/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. 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 {ENCFF521HYH|/files/ENCFF521HYH/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC2 value of 7.88. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF018FHH|/files/ENCFF018FHH/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of 1.73 and a self consistency ratio of 4.49. 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 {ENCFF893DLM|/files/ENCFF893DLM/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of 1.73 and a self consistency ratio of 4.49. 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_ENCSR000BVG | float |
TF_ChIP-seq_ENCSR000BVG |
TF_ChIP-seq ENCSR000BVG [biosample_summary="Homo sapiens SK-N-SH" and target="RXRA"]
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[5.18, 332] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF018FHH.bed.gz | 300.04 KB | 6fd93c4d023640d1f5bf1972ae6a0e84 |
| ENCFF018FHH.bed.gz.dvc | 100.0 B | 91a73da15a74d86f02393f601693860f |
| ENCFF018FHH.tabix.bed.gz | 216.6 KB | 811e6373ac302ecc16dc51bb55769dc1 |
| ENCFF018FHH.tabix.bed.gz.dvc | 106.0 B | 055c6c05c021d5997161e0e398c82ecd |
| ENCFF018FHH.tabix.bed.gz.tbi | 111.9 KB | 5a468b32dc35cea978dc7d1b05eda0ad |
| ENCFF018FHH.tabix.bed.gz.tbi.dvc | 110.0 B | 0a86adb78417ec7b24bc49f3e61c6bcd |
| genomic_resource.yaml | 4.46 KB | 4eb3ea80385b2b117b48d38ae47cc5d3 |
| genomic_resource_original.yaml | 4.36 KB | 5c8ffbe4ca997ff1cc9d8d61409a90cf |
| statistics/ |