TF_ChIP-seq_ENCSR000BUW
TF_ChIP-seq ENCSR000BUW [biosample_summary="Homo sapiens HL-60" and target="SPI1"]
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| Id: | TF_ChIP-seq/ENCSR000BUW |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000BUW [biosamplesummary="Homo sapiens HL-60" and target="SPI1"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN045IJI|/analyses/ENCAN045IJI/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF436BMH|/files/ENCFF436BMH/} processed by ChIP-seq ENCODE3 hg19 pipeline has 15691704 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting SPI1-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 {ENCFF822WIL|/files/ENCFF822WIL/} processed by ChIP-seq ENCODE3 hg19 pipeline has 18251496 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting SPI1-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 {ENCFF822WIL|/files/ENCFF822WIL/} 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 {ENCFF822WIL|/files/ENCFF822WIL/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.58. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF963KJK|/files/ENCFF963KJK/}, {ENCFF567RGM|/files/ENCFF567RGM/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.55 and a self consistency ratio of 3.19. 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 {ENCFF037MFL|/files/ENCFF037MFL/}, {ENCFF587OBC|/files/ENCFF587OBC/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.55 and a self consistency ratio of 3.19. 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_ENCSR000BUW | float |
TF_ChIP-seq_ENCSR000BUW |
TF_ChIP-seq ENCSR000BUW [biosample_summary="Homo sapiens HL-60" and target="SPI1"]
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[4.99, 487] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF587OBC.bed.gz | 1009.77 KB | cba9d4271e9a0b4f2f4e5cdbdb04fa29 |
| ENCFF587OBC.bed.gz.dvc | 101.0 B | 15ed027b5e018007ddd03d22e2677679 |
| ENCFF587OBC.tabix.bed.gz | 734.47 KB | 3c45a6584bc6d36c01c4582126a00a93 |
| ENCFF587OBC.tabix.bed.gz.dvc | 106.0 B | f28c1937aee9013f71dbc7a2c86f5e5e |
| ENCFF587OBC.tabix.bed.gz.tbi | 347.23 KB | 56c3f3c1d56185809cf59bb5a62a4ccd |
| ENCFF587OBC.tabix.bed.gz.tbi.dvc | 110.0 B | 9058695ff7a5a40fcf967b7ef6e239da |
| genomic_resource.yaml | 4.75 KB | 5b8a25816424ccdff132feb3157fcac2 |
| genomic_resource_original.yaml | 4.66 KB | 508154574fda99eacfaa63b588d5495d |
| statistics/ |