This readme describes how to use the software SOAPsplice.
For more information about SOAPsplice, please refer to the website: http://soap.genomics.org.cn


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Files:
./bin/: executable files.
./example/: example to use the software, you can just run the script "example.sh".
./doc/: document for users, it introduces the format of output files.


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How to use SOAPsplice to do alignment (with DNA) for transcriptome?

1. Build index for reference

% ./2bwt-builder <FASTA sequence file> <Output index prefix>

Example: % ./2bwt-builder humangenome.fa
      or % ./2bwt-builder humangenome.fa index/humangenome.fa  # the index files will be in the directory "index/".

Note:
a) Make sure that the file "2bwt-builder.ini" is together with "2bwt-builder". 
b) If you don't input "<Output index prefix>", a collection of files will be built with the filename prefix "<FASTA sequence file>.index", otherwise the prefix is "<Output index prefix>.index".



2. Do the alignment

% perl runsoapsplice.pl  -D <2BWT index prefix> -fq1 <reads_a> -fq2 <reads_b> -l <length of reads> -key <key name for all the outputs>  [Advanced Options] 

Example: % pelr runsoapsplice.pl -D hg18.fa.index -fq1 1.fq -fq2 2.fq -o ./ -key test -l 50

Note:

a) For the value of parameters, the value followed "-t" is the longest distance between two segments on the same chromosome(two segments belong to one read). For human, the recommended value is 500000, for arabidopsis, the recommended value is 1000. For "-m" and "-g", you can use the vaule in the example. For more information about SOAPsplice, please refer to the website: http://soap.genomics.org.cn.



If there are any further questions, please email to sbhuang1986@hotmail.com ,  soap@genomics.org.cn or zhangjinbo@genomics.org.cn
Date: Jan, 2011