Metadata-Version: 1.1
Name: SMART-BS-Seq
Version: 1.4.2.20150517
Summary: Specific Methylation Analysis and Report Tool for BS-Seq data
Home-page: http://methymark.edbc.org/SMART/
Author: Hongbo Liu
Author-email: hongbo919@gmail.com
License: UNKNOWN
Description: ========================
        README for SMART (1.4.2)
        ========================
        Time-stamp: <2015-05-17 11:28:37 Hongbo Liu>
        
        Introduction
        ============
        
        It is known that DNA methylation plays important roles in regulation
        of cell development and differentiation. DNA methylation/unmethylation
        mechanisms are common in all tissue/cell. However, different cell 
        types with the same genome have different methylomes. Recently,
        high-throughput sequencing combining bisulfite treatment (Bisulfite
        -Seq) have been used to generate DNA methylomes from a wide range of
        human tissue/cell types at a genome-wide perspective. To characterize
        the genome regions that consist of continuous CpGs with similar 
        methylation specificity, we developed the Specific Methylation Analysis
        and Report Tool (SMART) based on the quantified methylation specificity,
        Euclidean distance and similarity entropy, for identifying and 
        characterizing sets of genome segments comprising continuous CpGs with 
        similar methylation specificities. For a given set of multiple methylomes 
        profiled using BS-Seq, entropy-based procedures facilitated the quantification 
        of methylation specificity for each CpG and the determination of the 
        Euclidean distance and similar entropy for each pair of neighboring CpGs. 
        Subsequently, continuous scanning based on these quantified parameters 
        segments the genome into primary segments comprising CpG sites with high 
        methylation similarities across all cell types. Further, the 
        primary segments in close proximity and sharing similar methylation 
        patterns were merged into larger segments of different types, including 
        high specificity (HighSpe), low specificity (LowSpe) and almost no 
        cell-specificity (NoSpe) segments. Eventually, the High/LowSpe segments 
        with specific hypo-/hypermethylation in the minority of cell types, 
        cell-type-specific hypomethylation marks (HypoMarks) and cell-type-specific 
        hypermethylation marks (HyperMarks), were identified using a statistical 
        method. To facilitate the mining of methylation marks (MethyMarks) across 
        cell types and species, all algorithms used in this procedure were 
        integrated into a Specific Methylation Analysis and Report Tool (SMART), 
        which is also available at http://fame.edbc.org/smart.
        
        Install
        =======
        
        Please check the file 'INSTALL' in the distribution.
        
        Usage of SMART
        ==============
        
        :usage: SMART MethyDir CytosineDir [-h] [-n PROJECTNAME] [-o OUTPUTFOLDER] [-v]  
        
        
        
        positional arguments
        -----------------------
        MethyDir
        ```````````````
        The directory (such as /liuhb/BSSeq/) of the folder including methylation data files formated in wig.gz (such as H1.wig.gz). REQUIRED.
        
        CytosineDir
        ``````````````````
        The directory (such as /liuhb/CLoc_hg19/) of the folder including cytosine location files for all chromesomes formated in txt.gz (such as chr1.txt.gz). REQUIRED.
        
        optional arguments
        ----------------------
        -h, --help
        ``````````````````
        show this help message and exit
        
        -n PROJECTNAME
        `````````````````````````````
        Project name, which will be used to generate output file names. DEFAULT: "SMART"
        
        -o OUTPUTFOLDER
        ````````````````````````````````
        If specified all output files will be written to that directory. Default: the directory named using projectname and currenttime (such as SMART20140801132559) in the current working directory.
        
        -v, --version
        ```````````````````
        show program's version number and exit
        
        Example
        ==============
        
        Example data
        ---------------
        
        The example data can be found in the directory Example under the installation directory of SMART. It should be noted that the location of installation directory of SMART may be different in different Operating System. The Cytosines and their methylation level in 50kb regions from chr3 and chr6 were extracted for test of SMART. User can use following command to test SMART.
        
        Example command
        ---------------------
        :For Linux: 
        
        The main function SMART may be in /usr/local/bin/, and example data may be in ../python2.7/dist-packages/SMART/Example. The following referece may be useful for test of SMART::
        
          SMART /usr/local/lib/python2.7/dist-packages/SMART/Example/BSSeq_fortest/ /usr/local/lib/python2.7/dist-packages/SMART/Example/CLoc_hg19_fortest/ -n Test -o /usr/local/lib/python2.7/dist-packages/SMART/Example/Example_Results/
        
        
        
        :For windows: 
        
        The main function SMART may be in ..\\Python27\\Scripts\\, and example data may be in ..\\Python27\\Lib\\site-packages\\SMART\\Example. The following referece may be useful for test of SMART::
        
          cd  ..\Python27\Scripts\
          python SMART ..\Python27\Lib\site-packages\SMART\Example\BSSeq_fortest\ ..\Python27\Lib\site-packages\SMART\Example\CLoc_hg19_fortest\ -n Test -o ..\Python27\Lib\site-packages\SMART\Example\Example_Results\
        
        
        Output Files 
        ==============
        1. Folder SplitedMethy is a a output directory to store the splited Methylation data.
           The methylation data are stored in different chromosome sub-folders. In each
           sub-folder, the methylation data for all samples are included. 
        2. Folder MethylationSpecificity is a output directory to store the methylation
           levels and specifity for each C which is common across all samples. These files are
           stored in chromosomes. In this folder, MethylationSpecificity.wig.gz includes
           the methylation specifity of all common C. And this file can be uploaded to UCSC
           browser for visualization.
        3. Folder MethylationSegment includes three sub-folders: GenomeSegment, GenomeSegmentMethy,
           and MergedGenomeSegment. The sub-folder GenomeSegment stores all small segments
           identified by SMART in each chromosome. And the sub-folder GenomeSegmentMethy stores
           the methylation levels of each small segments across all samples which may be useful for
           users' local further analysis. The sub-folder MergedGenomeSegment stores the larger 
           segments merged based on the small segments in each chromosome. The final results are
           generated based on these merged segments.
        4. Folder FinalResults includes all intresting results which may be concerned by users.
           In this folder, there are six files. 
        
           -The first file 1SmallSegmentBed.txt.gz stores all small segments in bed format,  which  can be uploaded to UCSC browser for visualization.
        
           -The second file 2MergedSegmentBed.txt.gz stores all merged segments in bed format, which  can be uploaded to UCSC browser for visualization.
        
           -The third file 3MergedSegment.txt stores all merged segments in txt format, which is useful  for local further analysis.
        
           -The fourth file 4MergedSegmentwithmethylation.txt stores the methylation levels of all  merged segments across all samples, which is useful for local further analysis.
        
           -The fifth file 5MergedHighLowSpeSegmentwithspecificity.txt stores the methylation specificity and p values of t-test for each merged HighSpe/LowSpe segement, which is useful for further analysis on cell-type-specificity for each HighSpe/LowSpe segement. The positive p value represents the segment is hyper-methylated in the corresbonding cell-type, while the negative p value represents the segment is hypo-methylated in the corresbonding cell-type.
        
           -The sixth file 6CellTypeSpecificMethymarkPvalue.txt is a reformated file for the fifth file. In this file, only the HighSpe/LowSpe segements which show significant hypo- or hyper-methylation in some cell-types are remained. This file is usefull for users to select and analyze cell-type-specific methylation marks including HypoMarks and HyperMarks.
        
        Other useful links
        ==================
        :Predefined C locations in various species and other resources: http://fame.edbc.org/smart/
        :QDMR: http://bioinfo.hrbmu.edu.cn/qdmr/
        :UCSC Genome browser:  http://genome.ucsc.edu/
        
        Contact 
        ==================
        :For any help:  you are welcome to write to Hongbo Liu (hongbo919@gmail.com).
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Environment :: Web Environment
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: Python Software Foundation License
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python
