Resource
| Id | TF_ChIP-seq/ENCSR000ALJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000ALJ [biosample_summary="Homo sapiens keratinocyte female" and target="CTCF"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2, Rep 3 summary: female output_type: conservative IDR thresholded peaks audit_error: Processed alignments file {ENCFF012QCG|/files/ENCFF012QCG/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 4824171 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-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_error: Processed alignments file {ENCFF035SXH|/files/ENCFF035SXH/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 3833119 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-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_error: Processed alignments file {ENCFF756YJE|/files/ENCFF756YJE/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 2529297 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-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_internal_action: Released analysis {ENCAN431RTN|/analyses/ENCAN431RTN/} has in progress subobject document {ff88aa16-be9d-480c-9bdd-745949c896db|/documents/ff88aa16-be9d-480c-9bdd-745949c896db/} audit_internal_action: Released analysis {ENCAN431RTN|/analyses/ENCAN431RTN/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-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 {ENCFF012QCG|/files/ENCFF012QCG/} processed by ChIP-seq ENCODE4 v1.5.1 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 {ENCFF012QCG|/files/ENCFF012QCG/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.45. 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 {ENCFF756YJE|/files/ENCFF756YJE/} processed by ChIP-seq ENCODE4 v1.5.1 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 {ENCFF756YJE|/files/ENCFF756YJE/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.69. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000ALJ | float |
TF_ChIP-seq_ENCSR000ALJ |
TF_ChIP-seq ENCSR000ALJ [biosample_summary="Homo sapiens keratinocyte female" and target="CTCF"]
|
 |
[2, 447] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 11564773 | 0.36% | 45028 |
| chr1 | 1120065 | 0.45% | 4373 |
| chr2 | 891792 | 0.37% | 3462 |
| chr3 | 734110 | 0.37% | 2835 |
| chr4 | 526616 | 0.28% | 2056 |
| chr5 | 605644 | 0.33% | 2342 |
| chr6 | 661513 | 0.39% | 2564 |
| chr7 | 573974 | 0.36% | 2214 |
| chr8 | 492074 | 0.34% | 1921 |
| chr9 | 493144 | 0.36% | 1879 |
| chr10 | 531637 | 0.40% | 2078 |
| chr11 | 647506 | 0.48% | 2572 |
| chr12 | 597425 | 0.45% | 2320 |
| chr13 | 253165 | 0.22% | 971 |
| chr14 | 375624 | 0.35% | 1455 |
| chr15 | 382636 | 0.38% | 1512 |
| chr16 | 376834 | 0.42% | 1500 |
| chr17 | 559789 | 0.67% | 2207 |
| chr18 | 238009 | 0.30% | 917 |
| chr19 | 436507 | 0.74% | 1739 |
| chr20 | 331494 | 0.51% | 1289 |
| chr21 | 124479 | 0.27% | 476 |
| chr22 | 236054 | 0.46% | 925 |
| chrX | 374682 | 0.24% | 1421 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 45028 | 1 | 593 | 256.84 | 250 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF351YOQ.bed.gz | 670.69 KB | 3a1cc7e961c8f040a65bfb44c5428d8a |
| ENCFF351YOQ.tabix.bed.gz | 523.3 KB | c4e26b6ff40f75b718f3f0e3123587c2 |
| ENCFF351YOQ.tabix.bed.gz.tbi | 260.1 KB | 10f2eb0a17fb4558e2c02c8565fc6900 |
| genomic_resource.yaml | 5.58 KB | f58c148a3cc8880f7f4a08d0dd150fc7 |
| statistics/ |