SwDMR
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Application data |
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| Created by | Xianfeng Li |
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| Biological application domain(s) | Sequencing, Epigenetics, DNA methylation |
| Principal bioinformatics method(s) | Methylation calling |
| Technology | Any |
| Created at | Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou 325035, China |
| Maintained? | Yes |
| Input format(s) | Others |
| Output format(s) | Regions, Wiggle, PDF, SVG |
| Software features | Differentially methylated regions identification and annotation |
| Programming language(s) | Perl, R |
| Licence | GPLv3 |
| Operating system(s) | Linux, UNIX |
Summary: swDMR: a sliding window approach to identify differentially methylated regions based on bisulfite sequencing
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Description
swDMR is a sliding window approach, which is used to identify differentially methylated regions (DMRs) 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. It is flexible to identify DMRs from samples with several options. 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 DMRs visualization.
To successfully run this software, Perl v5.8.8 or later and R 2.12.0 or later are recommended.
Input file
Example:
The methylation of RRBS input files and other annotation files can be download at: [1]
Two methylation input files: Cancer.RRBS.cout.gz, Normal.RRBS.cout.gz Three annotation files: cpgIslandExt.txt, gene.bed, UTR_CDS_Intron_Upstream_Downstream.bed
The format of following information files are separated by table "\t".
1.The methylation input file format:
Chromosome Position Strand Context_of_C methylated_number unmethylated_number
2.gene.bed file format:
Chromosome start end geneName strand NM_number
3.UTR_CDS_Intron_Upstream_Downstream.bed format:
Chromosome start end element strand geneName
4.cpgIslandExt.txt can be download at: [2]
Commond: cd /path/of/swDMR perl ./swDMR --samples Normal.RRBS.cout.gz,Cancer.RRBS.cout.gz --name Normal,Cancer --outdir example/ChiSquare --statistics ChiSquare --cytosineType CG --window 1000 --stepSize 100 --pvalue 0.01 --coverage 4 --fold 2 --diff 0.1 --fdr 0.05 --processes 10 --Rbin /usr/bin/R --chromosome 1 --position 2 --ctype 4 --methy 7 --unmethy 8 --annotation ./UTR_CDS_Intron_Upstream_Downstream.bed --CGI cpgIslandExt.txt --gene gene.bed --left 1000 --right 1000
Change log
swDMR-1.0.0
--Xfliwz 01:51, 11 September 2012 (PDT): Renew the statistics.pm file
--Xfliwz 20:08, 11 September 2012 (PDT): Fixed bug track of CGI in swDMRmap.pm
swDMR-1.0.1
--Xfliwz 09:34, 17 October 2012 (PDT): Adjust the length of DMRs and add depth information in DMR result
--Xfliwz 16:51, 18 October 2012 (PDT): Fixed bug of the way of sliding in SlidingAndCreatWig.parallel.pl
swDMR-1.0.2
--Xfliwz 12:12, 24 October 2012 (PDT): Change the method of extension in Extend.pl
swDMR-1.0.3
--Xfliwz 14:09, 29 Novenber 2012 (PDT): Fixed the bug of 'cat' for cat-ting large number of files in SlidingAndCreatWig.parallel.pl
swDMR-1.0.4
--Xfliwz 17:29, 29 December 2012 (PDT): Use pspline (a R package) to draw DMR related points with simulation curves
swDMR-1.0.5
--Xfliwz 17:29, 15 June 2013 (PDT): Change the p value adjust method
Links
References
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