the easy Way

1. Verify the input files are in place. See RATools Input Files for more info.

2. Verify your run_all.pl script is up to date and configured for array and scanner specifications.

3. Execute:

   >perl run_all.pl DIRNAME
   

4. See RATools Output Files for a description of the output.

Configuring run_all.pl

A variety of parameters are adjustable in the run_parameter_search.pl script. If you are running the program for the first time you will typically need to adjust at least the gid alignment parameters.

Grid Alignment Parameters

• col_width : the width in pixels of an isolated feature

• row_width : the height in pixels of an isolated feature

Data Type Parameters

• outputFasta :

• haploid :

• primersUsed :

• numSegs :

• offset :

• rewriteFasta :

• dirname :

• LQvsCDF :

Basecalling Parameters

• totThresh : The total quality score threshold that a given base has to exceed to be called. Increasing this value requires increased support for basecalls. As a consequence, fewer bases are called. Bases that fail to reach this thresold are callled "N."

• strThresh : The strand minimum score. Sets a threshold governing the degree to which different strands can support different hypotheses. Decreasing this value reduces the degree to which the forward/reverse strands can differ, hence, reducing the number of bases called. If this threshold is exceeded, the base will be called "N".

Final Reliability Rules Parameters

• nInvalidateBase : defines the proportion of samples that can fail at a given site. If this threshold is exceeded, the given base in all samples is called "N".

• nInvalidateFrag : defines the proportion of bases that can fail withing a given PCR product. If this threshold is exceeded, all the bases in the PCR product are called "N".

• winSize : defines the size of a neighborhood window.

• failThresh : defines the proportion of bases in a neighborhood window (defined by $winSize) that can fail. If this threshold is exceeded, all the bases in the window are called "N".