/*lncRScan v0.1*/
/*Author: Lei Sun*/
/*Email: sunluky@gmail.com*/

==Introduction==
lncRScan (long non-coding RNA Scan) is a pipeline consists of five steps for detecting novel long non-coding RNAs from a set of candidate transcripts annotated by Cuffcompare.

==Steps of lncRScan==
Step 1 'extract_category'-- extract several categories of transcripts, which may contain lncRNAs. The candidate categories can be `i' (a transfrag falling entirely within a reference intron), 'j' (potentially novel isoform), 'o'
(generic exonic overlap with a reference transcript) and 'u' (intergenic transcript).
Step 2 'extract_length'-- extract the transcripts having long exonic length (>200nt).
Step 3 'extract ORF'-- exclude the assemblies that have long (�>300nt) putative ORF.
Step 4 'extract PhyloCSF'-- PhyloCSF was recruited to filter the transcripts of protein-coding potential from an evolutionary view.
Step 5 'extract Pfam'-- exclude transcripts with significant domain hits by searching Pfam.

==Install==
1) OS requirement - Unix/Linux

2) Steps
   -- Download "lncrscan" which contains three folders to your home directory MY_DIR (e.g. YOUR_DIR/lncrscan-read-only).
      $ svn checkout http://lncrscan.googlecode.com/svn/trunk/ lncrscan-read-only
   -- Set environmental variables on you OS by modifying .bashrc
      export PATH=$PATH:/MY_DIR/scripts
      export PERL5LIB=$PERL5LIB:/MY_DIR/lib
   -- Use the new environmental variables
      $ source .bashrc
   -- Make all scripts executable by
      $ chmod 0775 /MY_DIR/script/*
      
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