Published March 1, 2024
| Version 1.0.0
Dataset
Open
Semi-simulated TF pertubation in ATAC-seq datasets (Pertubation strength)
Description
Semi-simulated ATAC-seq data with TF pertubations of different pertubation strength. The three .tar-files contain:
- DTFAB_sim_es_beds.tar.gz: .bed files of the semi-simulated ATAC-seq fragments
- DTFAB_sim_cm.tar.gz: count matrices (per peak counts of semi-simulated fragments)
- DTFAB_sim_peaks.tar.gz: .bed files with ATAC-seq peak coordinates of semi-simulated fragments
The folder structure of 1.,2. & 3. is of the following format <tf>_<pertubation paradigm>_<pertubation_strength>. The corresponding files without any pertubation introduced can be found under data_baseline (peaks in peaks/merged_peaks.narrowPeak). The original samples were retrieved from ENCODE with following IDs: ENCFF495DQP, ENCFF130DND, ENCFF447ZRG, ENCFF966ELR, ENCFF358GWK, ENCFF963YZH. ChIP-seq peaks used to introduce perturbations correspond to following ENCODE identifiers: ENCFF156OCY, ENCFF592UDD, ENCFF250FJC, ENCFF500EWB.
This semi-simulated datasets is belongs to a series of datasets:
| Dataset | Description | DOI |
| I. pertubation strength (this) | TF pertubation with different strengths, no biases introduced | 10.5281/zenodo.10732704 |
| II. pos control | TF pertubation only introduced in (ChIP-) peaks with a motif of the respective TF. | 10.5281/zenodo.10781849 |
| III. fld | TF pertubation with additionally introduced fragment length distribution bias | 10.5281/zenodo.10781109 |
| IV. gc | TF pertubation with additionally introduced GC content bias | 10.5281/zenodo.10781759 |
Files
Files
(37.1 GB)
| Name | Size | Download all |
|---|---|---|
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md5:f2b01e24fed6b41d9d0458ae587b6abd
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36.9 GB | Download |
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md5:8fd26fa1dac120c55047827a9b055754
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105.9 MB | Download |
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md5:9ad2e856335f6ad3e6c57ff585646d0a
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41.2 MB | Download |
Additional details
Related works
- Is variant form of
- Dataset: 10.5281/zenodo.10781849 (DOI)
- Dataset: 10.5281/zenodo.10781109 (DOI)
- Dataset: 10.5281/zenodo.10781759 (DOI)
- References
- Data paper: 10.1038/nature11247 (DOI)