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swDMR: A sliding window approach to identify differentially methylated regions from whole genome bisulfite sequencing. https://www.ncbi.nlm.nih.gov/pubmed/26176536 https://sourceforge.net/projects/swdmr/ Software discription swDMR is a sliding window approach, which is used to identify differentially methylated regions (DMR) from bisulfite sequencing dataset at single base resolution. The dataset, like whole genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) with the same coverage region of samples, are suitable for swDMR. This software integrated several useful statistics methods, satisfying to two or multiple samples test. In addition, swDMR provides genomic features annotation with BED or GFF file. It can also produce WIG format file to upload to UCSC genome browser for DMR visualization. Platform and environment System: Linux or UNIX Software: perl >= v5.8.8, R >= 2.12.0 and BEDTools are required. How to run swDMR 1. Install >cd /path/of/swDMR----- Go to path of swDMR software installed >tar xzvf swDMR-xxx.tar.gz >cd swDMR-xxx >sh install ### tips: If you see some warns, when you install the dependence packages of swDMR. It may be that the packages in our swDMR are too old for your system. You can download the latest packages for installation as the file 'install'. Sorry for the problem! We will solve this in the future. 2. Run the software >cd swDMR-xxx >./swDMR --help Discription: This program is used to detect DMRs, which can also annotate DMRs through user's defination of BED format file. Usage: Input methylation file format: must contain follow information (separated by table "\t") you can assign the corresponding information contained in your files information required: chromosome position ctype methyl_reads unmethy_reads Example: ./swDMRs [options] < ... > swDMR --samples ESFibro.chr1.cout.gz,Fibro.chr1.cout.gz --name ESFibro,Fibro --outdir outdir --statistics Fisher --cytosineType CG --window 1000 --stepSize 100 --length 100 --pvalue 0.01 --coverage 4 --fold 2 --fdr 0.05 --Rbin /usr/bin/R --chromosome 1 --position 2 --ctype 4 --methy 7 --unmethy 8 -a UTR_CDS_Intron_Upstream_Downstream.bed -g gene.bed --CGI cpgIslandExt.txt Basic swDMR options: -h | --help print this help information on screen -sam | --samples input samples' methylation files separated by comma "," < a,b,c,...,g,h > -na | --name input samples' names separated by comma "," < a,b,c,...,g,h > -chp | --chromosome column of chromosome in your file, default <1> -pos | --position column of position in your file, default <2> -cp | --ctype column of cytosine type in your file, default <4> -mp | --methy column of methy reads in your file, default <5> -up | --unmethy column of unmethy reads in your file, default <6> -o | --outdir swDMR result directory -co | --coverage lowest coverage of cytosine reads to use, default <4> -s | --statistics choose one method to detect DMRs < T_test||Kolmogorov||Fisher||ChiSquare||Wilcoxon||ANOVA||Kruskal > if input samples == 2 --statistics should choose < T_test||Kolmogorov||Fisher||ChiSquare||Wilcoxon > if input samples >= 3 -statistics could choose < ANOVA||Kruskal > -CT | --cytosineType cytosine type < C|CG||CHG||CHH > -w | --window a sliding window to statistics, default <1000> -N | --points lowest number of selected type of cytosine in the window, default <10> -z | --stepSize step size of the sliding processes, default <100> -f | --fold max/min methylation level difference -d | --diff value of max-min methylation level -len | --length lowest length to join two fragment into one, default <100> -V | --pvalue p value to judge as a DMR, default <0.01> -R | --Rbin R bin -fdr fdr to adjust DMR p value, default <0.05> -pro | --processes parallel processes for DMR test and annotation, default <1> Annotation and DMR maps: -a | --annotation your annotation file should be bed of GFF format < BED||GFF > -g | --Gene BED file of gene coordinates --CGI cpgIsland file: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/cpgIslandExt.txt.gz. The other release or species cpgIsland file can also be downloaded from UCSC genome browser --left left side length of DMR in a map, default <1000> --right right side length of DMR in a map, default <1000> ## output fomart https://github.com/xflicsu/swDMR/wiki/About-swDMR#output-of-swdmr
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