TF_ChIP-seq_ENCSR000BIB
TF_ChIP-seq ENCSR000BIB [biosample_summary="Homo sapiens GM12892" and target="TAF1"]
×
| Id: | TF_ChIP-seq/ENCSR000BIB |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000BIB [biosamplesummary="Homo sapiens GM12892" and target="TAF1"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN614KAE|/analyses/ENCAN614KAE/} has in progress subobject document {485c28c2-4d1e-4e18-87c5-4ea625bcf5e4|/documents/485c28c2-4d1e-4e18-87c5-4ea625bcf5e4/} audit_internal_action: Released analysis {ENCAN614KAE|/analyses/ENCAN614KAE/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF370BIB|/files/ENCFF370BIB/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 14356474 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting TAF1-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 {ENCFF063XWS|/files/ENCFF063XWS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 13890074 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting TAF1-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 {ENCFF370BIB|/files/ENCFF370BIB/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF370BIB|/files/ENCFF370BIB/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.22. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF594SQR|/files/ENCFF594SQR/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 1.28 and a self consistency ratio of 2.04. 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_ENCSR000BIB | float |
TF_ChIP-seq_ENCSR000BIB |
TF_ChIP-seq ENCSR000BIB [biosample_summary="Homo sapiens GM12892" and target="TAF1"]
|
|
[4.99, 405] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF594SQR.bed.gz | 208.27 KB | 2d2820288a2a15118d9df787eb7c8436 |
| ENCFF594SQR.bed.gz.dvc | 100.0 B | d0380c06f5d20ec8e4f66de5a36cc291 |
| ENCFF594SQR.tabix.bed.gz | 150.64 KB | 51a5ce3b383ac76e0149d313492b7207 |
| ENCFF594SQR.tabix.bed.gz.dvc | 106.0 B | ffdd4b35b8603945921ac2d0205a67cc |
| ENCFF594SQR.tabix.bed.gz.tbi | 83.63 KB | 17680f527e056d473958ce2927b9c76f |
| ENCFF594SQR.tabix.bed.gz.tbi.dvc | 109.0 B | d904c1d289e1a7da7b6bb46eb3b51acf |
| genomic_resource.yaml | 4.42 KB | 50f4c66751135a50123433bcbb4d49ea |
| genomic_resource_original.yaml | 4.32 KB | 65d4835ae75c9ae16fc69357029b60c7 |
| statistics/ |