#Verzijlbergen and Marston 2013:
Paper title : "Shugoshin biases chromosomes for biorientation through condensin recruitment to the pericentromere" Verzijlbergen et al. eLife 2014;3:e01374. DOI: 10.7554/eLife.01374
The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus (Edgar et al., 2002) and are accessible through GEO Series accession number GSE53856 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53856
Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Res. 2002 Jan 1;30(1):207-10
#Program Versions: Mapper: BWA Version: 0.6.1-r104
Reference Genome: sacCer3
Removal of duplicate reads: samtools Version: 0.1.16 (r963:234)
RPM scaling, bedgraph creation and bed intersections: bedtools v2.16.2
bedgraph to bigwig conversion: wigToBigWig v 4 (UCSC utilities)
workflow1.sh : initial mapping and processing
workflow-each-cen.sh : Plot data for each centromere
workflow-all-cen.sh : Plot all centromeres together as a boxplot per window
Cen-boxplot.pl : generates boxplot data binned around the centromere
EveryCen-boxplot.pl: Pairwise fold chage data binned around the centromere
plot-everyboxplot.r: Create the plots from EveryCen-boxplot.pl
AllCen.r : R script for plotting Cen-boxplot.pl
#Data files Most of the data in this repository is intended to be used as an example for the scripts. For the complete set of data please see the GEO identifier GSE53856: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53856
CENTROMERE.gff : Centromere locations
rDNA.bed : excluded region
bedgraphfiles.tgz : bedgraph files to be used with state 2 workflows