
The file "testseq" contains a set of potato EST sequences with cultivar
and tissue information in FASTA format, which were chosen randomly from 
TIGR potato database. The data have been aligned using CAP3, and can be
processed with QualitySNP.

1. First set the variable "program_path2" in the QualitySNPpipeline script
   to the directory where you have installed the QualitySNP programs.

   Additionally, you might want to set your "PATH" variable to include
   this program location (see the QualitySNP manual).


2. Now run the pipeline using the command:

   % QualitySNPpipeline testseq 95 4 2 30 0.75 0.8 0.2 0.5 2

   If you want to include the quality file, run the command:

   % QualitySNPpipeline -q testseq 95 4 2 30 0.75 0.8 0.2 0.5 2


3. Examine the output, in particular the files
   1. file "realsnpinfo" which includes all SNPs in the clusters, excluding
      those from single haplotypes;
   2. file "SNPquality" which includes all relevant information for identifying
      reliable SNPs, such as confidence scores and allele haplotype scores;
   3. file "availcontigwithSNP" which includes haplotype and SNP information
      for every contig, as well as statistical information.

   Please consult the manual for more details about the output files created.


Note 1: running the programs with quality information does not alter
the prediction, as the quality information is not used in the algorithm,
but is used only for displaying the nucleotide position's reliability.
      
Note 2: The sequences in the file "testseq" are obtained from the TIGR potato
database; according to our study, these sequences are not of good quality.
Please read our (submitted) paper for more information.

Note 3: allavailcontigseqwithSNP.fasty is the fasty results on the uniref100. 
This file is only used to test GetnonsySNP to analysis of fasty results and 
obtain non-synonymous SNPs, SNPs in coding or UTR etc.

Note 4: the directory of snpdb is the final results of QualitySNP, this data can be 
loaded into database by the script. Please test the program under usertesting 
directory. 
