TF_ChIP-seq_ENCSR036RHV
TF_ChIP-seq ENCSR036RHV [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens SAFB2" and target="SAFB2"]
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| Id: | TF_ChIP-seq/ENCSR036RHV |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR036RHV [biosamplesummary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens SAFB2" and target="SAFB2"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: genetically modified (insertion) using CRISPR targeting H. sapiens SAFB2 output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN185UNJ|/analyses/ENCAN185UNJ/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_internal_action: Released analysis {ENCAN185UNJ|/analyses/ENCAN185UNJ/} has in progress subobject document {86677d2b-3d13-47fc-bca4-bb1554db9666|/documents/86677d2b-3d13-47fc-bca4-bb1554db9666/} audit_warning: Processed alignments file {ENCFF161YXE|/files/ENCFF161YXE/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 18961126 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting SAFB2-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 {ENCFF523XZN|/files/ENCFF523XZN/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF523XZN|/files/ENCFF523XZN/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.97. 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 {ENCFF161YXE|/files/ENCFF161YXE/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF161YXE|/files/ENCFF161YXE/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.54. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF710TSK|/files/ENCFF710TSK/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline have a rescue ratio of 1.65 and a self consistency ratio of 3.33. 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 {ENCFF196QOW|/files/ENCFF196QOW/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline have a rescue ratio of 1.65 and a self consistency ratio of 3.33. 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_ENCSR036RHV | float |
TF_ChIP-seq_ENCSR036RHV |
TF_ChIP-seq ENCSR036RHV [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens SAFB2" and target="SAFB2"]
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[10.8, 393] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF710TSK.bed.gz | 213.55 KB | d538d5a35788e08003fe8e405bfec830 |
| ENCFF710TSK.bed.gz.dvc | 100.0 B | 441d6113db80c99e1456f728c82515c8 |
| ENCFF710TSK.tabix.bed.gz | 172.22 KB | 05f65517b6bdbf49e2b5dd705a1f601d |
| ENCFF710TSK.tabix.bed.gz.dvc | 106.0 B | 18ea9c737633e2c64986d1f04f0fc3d0 |
| ENCFF710TSK.tabix.bed.gz.tbi | 73.49 KB | 1f9db4dabe1d43fb4fdb67098ae7729f |
| ENCFF710TSK.tabix.bed.gz.tbi.dvc | 109.0 B | eed257cdc33684a256fe04f91c221a68 |
| genomic_resource.yaml | 5.97 KB | 39ab7baa2ac785090e07d930040a5860 |
| genomic_resource_original.yaml | 5.81 KB | 3d116dd1c7993b4a9668801e167ce583 |
| statistics/ |