riboshape Files

Copyright (c) 2016, Tzu-Yu J. Liu, Yun S. Song
All rights reserved.


%%%%%%%%%%%%%%%%%%%%%%%%%%%%% riboshape %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

How to run the software?


1. Preapre data structure in the folder 'data', e.g., 'data/chxdata.mat', 
which consists of the following variables.

GeneName: n by 1 cell, where n is the number of genes. Each cell contains 
          the name of the gene.
Asitecount: n by 1 cell. Each cell is a lg by 1 vector of the number of 
          ribosome footprint counts at each codon position, where lg 
          (unit: codon) is the length of the corresponding gene.
asite_density: n by 1 vector. The average number of ribosome footprint 
          counts of the corresponding gene.
CDS: n by 1 cell. Each cell contains the coding region sequence
codon: 64 by 1 cell. Each cell contains the name of the corresponding 
          codon. 
distribution: n by 1 cell. Each cell contains a 64 by lg binary matrix. 
          The order of the rows in the matrix should follow the order in 
          the variable codon.


2. Compute codon features (optional): You can precompute the codon 
feautres, if you skip this step, the program in setp 3 will detect the 
missing files and generate them. 

To compute the features, specify the name of the data structure prepared 
in step 1, in the file 'compute_codon_features.m' located in the folder 
'codon_features'. Set the bandwidths for kernel smoothing. And run the 
'compute_codon_features.m' file.

3. Predict density: Specify the name of the data structure and the range 
of transcript length in the file 'analysis.m' in the folder 
'density_prediction'.