Program: NSMAP (A Nonnegativity and Sparsity constrained Maximum A Posteriori model for Isoform identification from RNA-Seq)
Authors: Zheng Xia and Xiaobo Zhou
Company: The Methodist Hospital Research Institute
Version: 0.1.0
Date:    December, 2010


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Introduction
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NSMAP is a tool for inferring isoforms from RNA-Seq data which uses the sparsity constraint to
identify the real expressed isoforms from large candidate isoform sets constructed by combining putative exons.


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Starting
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Currently NSMAP is implemented in Matlab. Before running NSMAP, we need to preprocess the output of TopHat to provide the required input for NSMAP.
For data preprocessing, please refer the  "Data preprocessing" directory.

Run NSMAP_main.m by specifying the input_filename and output_filename where
the input_filename is the output in the "Data preprocessing" step.


The output of NSMAP is in gtf format which is similar with the output of Cufflinks.

column   	Example	Description
1		    Chromosome name
2	        NSMAP
3	        The type of record (always either "transcript" or "exon")
4	        The leftmost coordinate of this record (where 1 is the leftmost possible coordinate)
5	        The rightmost coordinate of this record, inclusive.
6	        1000
7	        strand	
8           gene id, isoform id and expression level

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Contacts:
If you want to contact authors, please send an e-mail to: zxia@tmhs.org