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README
 
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Usage Description
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The cisRCNEs identification pipeline is used to screen cis-regulatory conserved noncoding elements from 12way whole-genome alighnment
Six steps are performed as: 
(1) Retain the noncoding elements from mostCons elements; 
(2) Retain the cis-regulatory elements that located in collinear segments; 
(3) Retain >= minimal length elements from mostCons_nocoding_inColl elements; 
(4) Using maf_parse to extract elements alignments based on 12way alignments; 
(5) Using maf_parse to extract elements alignments based on 12way alignments; 
(6) Retain elements with minimal alignment identity from elements;

 
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Directory Contents
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This directory includes README, input directory, output directory and scripts directory. 
 
 
The sections below include:
 
	scripts directory
		maf_parse.pl
                run.sh
	Input directory
		cds_bed directory
		      cds.bed.sorted files
		mostCons directory
                      allMostCons.bed file
                      chr[1~7] directory
                         chr[1~7]-mostCons.bed 
                         chr[1~7]-scores.wig
                coll_segments directory
                         12way_cucumber.bed
                maf directory
                    12way.maf
                    chr_maf directory
                        chr[1-7].maf
	Output directory
		cisRCNEs.bed
	README file
 
 
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run.sh file
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scripts directory
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This directory provides the dependency perl scripts required in run.sh.
(1) maf_parse.pl was used to parse maf file and screen elements with minimal length and identity cutoff;
(2) run.sh was the main script of all six steps;

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Input directory
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This directory provides coding sequence annotation as bed files and 12way alignments with maf file and 12way collinear segments with bed files and mostCons elements identified by previous pipeline.

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Output directory
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This directory provides main output files including cis-regulatory conserved noncoding elements with maf blocks.



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README file
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It is this file.