Prediction of nucleosome dyads for the K562 cell line in the hg19 genome assembly
DOI10.5281/zenodo.3820875Zenodo3820875MaRDI QIDQ6723172
Dataset published at Zenodo repository.
Author name not available (Why is that?)
Publication date: 12 May 2015
Copyright license: No records found.
Predicting dyads from MNase-seq data I needed the location of nucleosomal dyads in the K562 cell line (ENCODE tier 1 line). Surprisingly, although plenty of MNase-seq data for that cell line is available, no nucleosome and dyad prediction exists. Running NuMap I found theNuMapsoftware by Anton Valouev to do exactly what I intended. Since it is in a somewhat obscure page and this seemed to be the only place where this software was, I haveuploaded it into a Github repositoryfor the sake of preservation (https://github.com/orphancode/NuMap). Predicting dyads from MNase-seq data with NuMap seemed trivial: I downloaded theK562 MNase-seq data set(11 replicates ~85Gb!!), combined all replicates and ran NuMap on the data(instructions on the Github README). From NuMap output there aredyad positions in bed formatand you can also produce several metrics to evaluate how good the prediction was. Distograms phasograms Valouev describes two measurements of the frequencies of distances between MNase-seq reads. The frequency of distances between reads mapping to opposite strands can be used to build a distogram, which ilustrates the expected nucleosome length (147 bp) - this is consistent across most eukaryotic cells. The frequency of distances between reads mapping to the same strand gives a measurement of the distance between nucleosomes, as theyre separated by some linker DNA - (Valouev calls this plot a phasogram). This measurement, on the other hand tends to be species and cell-type specific. K562 predictions: The expected 147 bp nucleosome length in K562 cells. The average distance between dyads in K562 cells seems to be 185 bp. References: Valouev, A., Johnson, S. M., Boyd, S. D., Smith, C. L., Fire, A. Z., Sidow, A. (2011). Determinants of nucleosome organization in primary human cells. Nature, 474(7352), 516520.http://doi.org/10.1038/nature10002
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