A tool for identifying miRNA-target interactions from CLIP-seq peaks

clipSearch is a tool for for identifying miRNA-target interactions from CLIP-seq peaks

Usage: clipSearch [options] <mir file, fasta> <peak, bed>
peak format is bed6+
[options]
-v/--verbose : verbose information
-V/--version : clipSearch version
-h/--help : help informations
-o/--output : output file
-m/--max-mfe : maximum mfe for miR-target duplex [default < 0]
-s/--min-score : minimum score for miR-target duplex [default > 0]

Download clipSearch.tar.gz from http://starbase.sysu.edu.cn/clipSearch/; unpack it, and make:
tar -xvf clipSearch.tar.gz
cd clipSearch
make
The newly compiled binary (clipSearch) is in the clipSearch /bin directory.

At this point you should have everything to run a built-in test data set.
cd test_data
./run_test.sh

Operating system: clipSearch is designed to run on POSIX-compatible platforms, including UNIX, Linux and Mac OS/X. We have tested most extensively on Linux and MacOS/X because these are the machines we develop on.
Compiler: The source code is compiled with the C++ compiler g++. We test the code using the g++ compilers. Libraries and other installation requirements: clipSearch includes one software library: the RNAfold library package. All will automatically compile during clipSearch installation process. By default, clipSearch does not require any additional libraries to be installed by you.

If everything goes well you can get started with your real data! :)
You need to have the reference genome
As an example, let's assume you use human genome (version hg19).
(1) Genome: wget -c 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/'
rm -f chrUn hap.fa.gz *random.fa.gz
mkdir genome
gzip ¨Cd .gz
cat chr.fa > genome/hg19.fa; cd..
(2) build the fai index:
samtools faidx genome/hg19.fa
(3) miRNA file
You can get the miR file from mirbase.org
(4)AGO CLIP-seq peaks
You can download the CLIP-seq peaks from starBase download center
http://starbase.sysu.edu.cn/download.php

bin/clipSearch ./test_data/testGenome.fa ./test_data/testGenome.fa.fai ./test_data/testMir.fa ./test_data/testPeak.bed >./test_data/test_clipSearch_mtis.txt

#chrom, chromStart, chromEnd, miR:peak, score, strand, seedType, mfe, alignScore, miR(3'-5'), pairs, target(5'-3'),
PDCD4 112 134 hsa-miR-21-5p:AGOPeak1 11.00 + 8mer -9.00 43.00

miRNA  3'--AGTTGTAGTCAGACTATTCGAT-5'
          -.:::.||-|.|||.||||||||
target 5'-AGTGGAAT-ATTCTAATAAGCTA-3'

Thanks a lot to everyone who contributed to the public code used by clipSearch.

/*******************************************************************************

• clipSearch - A tool for identifying miRNA-target interactions from CLIP-seq peaks
  
• Author : Jian-Hua Yang [email protected]
  
• School of Life Sciences, Sun Yat-Sen University
  
• Create Time: 18/09/2010
  *******************************************************************************/