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BM-Map 2.0.1

12/01/2011

For citation information, please go to Credits.

• Bowtie
• SAMtools
  
  

• Ji, Y, Xu, Y, Zhang, Q, Tsui, K-W, Yuan, Y, Liang, S, Norris, C, Liang, H. BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data. Biometrics.2011 Dec;67(4):1215-24. [PDF Full Text][Supplementary Info]
  
  

• Yuan Yuan
• Clift Norris
• Yanxun Xu
• Kam-Wah Tsui
• Yuan Ji*
• Han Liang*
  
  

• Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center
  
• Department of Biostatistics, MD Anderson Cancer Center
  
  

For command line option:

• Step 1: Prepare input file
• Step 2: Configure InputFile.txt
• Step 3: Run BM-Map from command line

 

For graphical user interface (GUI):

• Step 1: Prepare input file
• Step 2: Launch GUI
• Step 2: Specify parameters in the following window (equivalent as Configure InputFile.txt).



• Step 3: Click "Run" button to run BM-Map.

 

---

BM-Map has strict requirements for the input file format. Currently, the supported file formats are SAM for BM-Map 2.0.0,  and MAP (the default output format of Bowtie) for BM-Map 1.0.0. Many prominent mapping tools can output alignments in SAM format. However, we strongly recommend the Bowtie-produced SAM/Map format as the input for BM-Map, which has been extensively tested with the current version of BM-Map.  Bowtie produces SAM and/or Map format as output by simply specifying options on its command line ( See Bowtie website for more details).

---

Inputfile.txt contains the parameters that are required for running BM-Map. Usually, users will need to specify the values of the following parameters:

• MAP_FILENAME
• LOG_FILENAME
• MAX_NUM_MISMATCHES_FOR_TOP_HITS
• EXTRA_NUM_MISMATCHES_FOR_ADDITIONAL_HITS
• SEQ_FLANKING_VALUE
• PROB_OUTPUT
• STRANDNESS_OPTION
• NUM_THREADS
• POLYMORPHISM_RATE

Items below are RARELY changed:

• TOTAL_ITERATIONS
• BURNIN_ITERATIONS
• NUM_PARTS
• PART_TO_RUN

For a detailed description and guidelines for above parameters, please refer to BM-Map Manual.

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1. Open a command-line window in Microsoft Windows (or open terminal in Linux/Mac), cd to the directory where BM-Map.exe and "inputfile.txt" are located.
2. On the command line (or terminal), for Mac/Linux version, type:
   ./BM_Map.exe InputFile.txt
   or for Windows version, type:
   .\BM_Map.exe .\Inputfile.txt
   Then press "return".

---

• For 64-bit Windows:
  Navigate to BM_Map folder and double click "Run.exe" to launch the GUI
  
  
• For Mac/Linux:
  1. Install mono for desired platform before proceed. Mono is a cross-platform, open source .NET development network. Mono for Mac and various distribution of Linux can be found at : http://www.go-mono.com/mono-downloads/download.html.
  2. Navigate to BM_Map directory.
  3. The users may need to get the permission for executing "Run.command" by typing the following in the terminal:
     chmod u+x Run.command
     
  4. Double click "Run.command" to launch the GUI.