icefoxx / methylmaps Goto Github PK
View Code? Open in Web Editor NEWThis project forked from epigenomics/methylmaps
Data analysis pipeline for the Methyl-MAPS method
License: GNU General Public License v3.0
This project forked from epigenomics/methylmaps
Data analysis pipeline for the Methyl-MAPS method
License: GNU General Public License v3.0
Methyl-Analyzer is a python package that analyzes genome-wide DNA methylation data from the methylation mapping analysis by paired-end sequencing (Methyl-MAPS) method. 1. Requirements =============== * Python - python 2.7 - numpy - pyfasta - pysam One easy way to install the above packages is to use 'pip'. For example, $ sudo pip install numpy 2. Installation =============== 2.1 Download Methyl-Analyzer from: http://github.com/epigenomics/methylmaps or clone the repository via git: git clone git://github.com/epigenomics/methylmaps.git 2.2 At the methylmaps directory, run the following command: $ python setup.py build $ sudo python setup.py install All data analysis scripts are stored under the python bin directory. 3. Pre-analysis data preparation ================================ Compile required annotation files for the data analysis pipeline 3.1 CpG/RE/McrBC sites * Input 1) chromosome name 2) fasta sequence for the chromosome * Example: $ parse_sites.py chr11 chr11.fa 4. Data Analysis Pipeline ========================= 4.1 Parsing paired-end reads * Input: 1) Paired-end reads sequenced by SOLiD platform. Note: the current parser works only for SOLiD mate-pair format. 2) Chromosome mapping file for mapping the chromosome IDs used in the mate-pair format file to the formal chromosome names. * Example: $ parse_mates.py --out_dir /path/to/frag_dir human.cmap \ re_reads.mates 4.2 Filtering methylated/unmethylated fragments * Input: 1) Parameters used in the filtering process. See the example parameter file at data/filter_para. 2) CpG/RE/McrBC annotation files (generated by 'parse_sites.py') 3) Parsed RE fragments (by 'parse_mates.py') 4) Parsed McrBC fragments (by 'parse_mates.py') * Example: $ filter.py --out_dir /path/to/filter_dir --para filter_para chr1 \ /path/to/anno_dir chr1_re chr1_mcrbc 4.3 Estimating CpG methylation probability * Input: 1) Global methylation level obtained by LUMA assay 2) Methylated/unmethylated information collected by 'filter.py' * Example: $ score.py --out_dir /path/to/meth_dir 0.71 chr1 247249719 \ /path/to/filter_dir/methdata_chr1 4.4 Alternative procedure Run the all-in-one script for data analysis from the beginning to the end * Input: 1) Parameters required for the pipeline. See example at data/pipeline_paras_hg18 2) RE reads in the mate-pair format 3) McrBC reads in the mate-pair format 4) Define output directory * Example: $ run_pipeline.py --format mates pipeline_paras_hg18 re_reads.mates \ mcrbc_reads.mates /path/to/out_dir --run 5. Visualization ================ Create BED, Microarray, and Wiggle format to visually check DNA methylation profiles. * BED tracks for CpG/RE/McrBC sites: use 'create_cpg_track.py' * BED tracks for RE/McrBC fragments: use 'create_frag_track.py' * Microarray tracks for DNA methylation profiles: use 'create_microarray_track.py' * Wiggle tracks for DNA methylation profiles: use 'create_wiggle_track.py' 6. Citation ================ Xin Y, Ge Y, Haghighi F. Methyl-Analyzer - Whole Genome DNA Methylation Profiling. Bioinformatics. 2011 Jun 17. [Epub ahead of print]
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.