open pcdh_bowtie3.m first

% The whole process need the file: 
% 1.cellranger output (5' end gene expression)
% 2.pcdhg 5'end sequencing data (clean reads .gzfile)
% 3.pcdhg exon 1 sequence as reference

% The whole process need the script:
% 1.pcdh_bowtie3.m, and get output, a sam file and a bam file.

% 2.use sam file and pcdhg sequencing data in this process:  pcdh_caculate1_3.m & fpcdh_caculate1.m; output: pcdh_caculate.csv

% 3.use pcdh_caculate.csv and cellranger output in this process: cell_barcode_correction1_3.m; output: pcdh_caculate_correction
 if you have more than 1 sequencing file, run the process above independently

% 4.pcdh_cal3_1.m & fpcdh_cal3.m;
 you can combine multiple sequencing files in this process.


% after these 4 process,you will get an pcdhg expression matrix calculated by UMI or reads.
% The rest process are describe in the other file



