TF_ChIP-seq_ENCSR000DZX
TF_ChIP-seq ENCSR000DZX [biosample_summary="Homo sapiens GM12878" and target="IRF3"]
×
| Id: | TF_ChIP-seq/ENCSR000DZX |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000DZX [biosamplesummary="Homo sapiens GM12878" and target="IRF3"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: File {ENCFF719MXF|/files/ENCFF719MXF/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_internal_action: Archived analysis {ENCAN761GUB|/analyses/ENCAN761GUB/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF935OOR|/files/ENCFF935OOR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 18691182 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting IRF3-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 {ENCFF519GVE|/files/ENCFF519GVE/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 13280733 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting IRF3-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 {ENCFF519GVE|/files/ENCFF519GVE/} processed by ChIP-seq ENCODE3 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 {ENCFF519GVE|/files/ENCFF519GVE/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.13. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF294WAI|/files/ENCFF294WAI/}, {ENCFF349ZBJ|/files/ENCFF349ZBJ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.34 and a self consistency ratio of 91.29. 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 {ENCFF719MXF|/files/ENCFF719MXF/}, {ENCFF823NYZ|/files/ENCFF823NYZ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.34 and a self consistency ratio of 91.29. 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: |
|
| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000DZX | float |
TF_ChIP-seq_ENCSR000DZX |
TF_ChIP-seq ENCSR000DZX [biosample_summary="Homo sapiens GM12878" and target="IRF3"]
|
|
[6.09, 232] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF719MXF.bed.gz | 40.21 KB | 8b84ec83c48271bb2b61da7e872c9821 |
| ENCFF719MXF.bed.gz.dvc | 99.0 B | 88369116e65efb8f571217a3c05eeb29 |
| ENCFF719MXF.tabix.bed.gz | 27.45 KB | 2159ea97c3866eb942263877dccb5907 |
| ENCFF719MXF.tabix.bed.gz.dvc | 105.0 B | adb90db8807e12ba0c1f6103469d7fd8 |
| ENCFF719MXF.tabix.bed.gz.tbi | 23.75 KB | 341e8d30bed69d45ed904fb9d821f8df |
| ENCFF719MXF.tabix.bed.gz.tbi.dvc | 109.0 B | d7755cb67534b185f52c6ad806467151 |
| genomic_resource.yaml | 4.96 KB | 726b59d417746b8204bbc2682a9dc402 |
| genomic_resource_original.yaml | 4.86 KB | e627417eed7ee5fd5591f3338d15acd8 |
| statistics/ |