TF_ChIP-seq_ENCSR785OKZ
TF_ChIP-seq ENCSR785OKZ [biosample_summary="Homo sapiens GM12878" and target="RB1"]
×
| Id: | TF_ChIP-seq/ENCSR785OKZ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR785OKZ [biosamplesummary="Homo sapiens GM12878" and target="RB1"] |
| Description: |
status: released biological_replicates: Rep 3, Rep 4 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN501BOT|/analyses/ENCAN501BOT/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} 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 {ENCFF750OED|/files/ENCFF750OED/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF750OED|/files/ENCFF750OED/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.11. 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 {ENCFF963AMS|/files/ENCFF963AMS/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF963AMS|/files/ENCFF963AMS/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.08. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF593XIS|/files/ENCFF593XIS/}, {ENCFF601XVA|/files/ENCFF601XVA/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.97 and a self consistency ratio of 3.72. 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 {ENCFF942SCN|/files/ENCFF942SCN/}, {ENCFF372WMI|/files/ENCFF372WMI/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.97 and a self consistency ratio of 3.72. 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_ENCSR785OKZ | float |
TF_ChIP-seq_ENCSR785OKZ |
TF_ChIP-seq ENCSR785OKZ [biosample_summary="Homo sapiens GM12878" and target="RB1"]
|
|
[14.5, 796] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF601XVA.bed.gz | 354.88 KB | 04fd5d92531b46908c2f3bf60b199d9a |
| ENCFF601XVA.bed.gz.dvc | 100.0 B | 169b8f72c5d84aed93ac39c823880290 |
| ENCFF601XVA.tabix.bed.gz | 257.88 KB | c87a74d2d6ce4e72cd7c387b18f48cf1 |
| ENCFF601XVA.tabix.bed.gz.dvc | 106.0 B | a19b4bd9a118f41727a16d608bbec798 |
| ENCFF601XVA.tabix.bed.gz.tbi | 120.64 KB | 9523d1836e392537f6a2ce78c4984b4e |
| ENCFF601XVA.tabix.bed.gz.tbi.dvc | 110.0 B | 57280835d511319082fdfb066a47faf6 |
| genomic_resource.yaml | 5.07 KB | 4c84d0cab6857c0ea5d6c54821e4626f |
| genomic_resource_original.yaml | 4.98 KB | fa7f35ed696c8b0500ae782d4a3f3bef |
| statistics/ |