Chodavarapu 2010, Nucleosome positioning in shoots.
Nucleosome maps (MNase-seq samples) and histon H3 map in
A. thaliana shoots grown under continuous light for
- Raw data was downloaded from: GEO
- Input file format: SRA
- Download date: 25-11-2016
From A. thaliana (Feb 2011 TAIR10/araTha1).
DNase FAIRE data:
FASTQ files were extracted from SRA files using fastq-dump
toolkit v2.5.0) and mapped to the genome
using Bowtie v0.12.8. SAM
files were then converted into bam
using samtools v0.1.14
and to bed using bamToBed v2.12.0
conversion was carried out using bed2sga.pl
(ChIP-Seq v. 1.5.2).
Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ, Casero D, Bernal M, Huijser P, Clark AT, Krämer U, Merchant SS, Zhang X, Jacobsen SE, Pellegrini M
Relationship between nucleosome positioning and DNA methylation.
Nature. 2010 Jul 15;466(7304):388-92. doi: 10.1038/nature09147. Epub 2010 May 30.
Relationship between nucleosome positioning and DNA methylation: Bisulfite-Seq, ChIP-Seq, and Mnase-Seq
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