Yardimci 2014, DNase-seq of naked DNA from two different cell types.
DNase-seq experiments on deproteinized naked genomic DNA
isolated from two different cell types (K562 and MCF7) to
determine sequence cleavage bias associated with the DNase-seq
- Raw data was downloaded from: GEO
- Input file format: SRA
- Download date: 9-3-2017
From H. sapiens (Feb 2009 GRCh37/hg19).
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).
Yardimci GG, Frank CL, Crawford GE, Ohler U
Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.
Nucleic Acids Res. 2014 Oct 29;42(19):11865-78. doi: 10.1093/nar/gku810. Epub 2014 Oct 7.
Explicit DNase sequence bias modeling enables high resolution transcription factor footprint detection