TF_ChIP-seq_ENCSR000BHU
TF_ChIP-seq ENCSR000BHU [biosample_summary="Homo sapiens HepG2" and target="RXRA"]
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| Id: | TF_ChIP-seq/ENCSR000BHU |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000BHU [biosamplesummary="Homo sapiens HepG2" and target="RXRA"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN964FSC|/analyses/ENCAN964FSC/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF799DNN|/files/ENCFF799DNN/}, {ENCFF964JXI|/files/ENCFF964JXI/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 2.11 and a self consistency ratio of 5.72. 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_not_compliant: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF145AUL|/files/ENCFF145AUL/}, {ENCFF071UJQ|/files/ENCFF071UJQ/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 2.11 and a self consistency ratio of 5.72. 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: Processed alignments file {ENCFF881TVG|/files/ENCFF881TVG/} processed by ChIP-seq ENCODE3 hg19 pipeline has 10305695 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 {ENCFF881TVG|/files/ENCFF881TVG/} 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 {ENCFF881TVG|/files/ENCFF881TVG/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.23. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BHU | float |
TF_ChIP-seq_ENCSR000BHU |
TF_ChIP-seq ENCSR000BHU [biosample_summary="Homo sapiens HepG2" and target="RXRA"]
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[4.79, 341] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF964JXI.bed.gz | 415.35 KB | d540c903680e4b4ac7aea04e684324a5 |
| ENCFF964JXI.bed.gz.dvc | 100.0 B | 63f920263a3b8bfad2286344775b7b74 |
| ENCFF964JXI.tabix.bed.gz | 305.37 KB | a4f56a3753ff61289822f4be314de30f |
| ENCFF964JXI.tabix.bed.gz.dvc | 106.0 B | 22a84bc40872260823ac4002abb82d4c |
| ENCFF964JXI.tabix.bed.gz.tbi | 151.17 KB | 666c46f68a8d71de8041696b8b2b53ad |
| ENCFF964JXI.tabix.bed.gz.tbi.dvc | 110.0 B | 2a081733e1e39025c3bbbc408846cfa9 |
| genomic_resource.yaml | 4.28 KB | 9ee1cac4f468f8c39c68b18f6df685dc |
| genomic_resource_original.yaml | 4.19 KB | a44a29b2b14ead16ecf8eb8e60b9cb1e |
| statistics/ |