File	Date	Author	Commit
example	2013-05-04	hakan	[6c1a73] Added Sample Control Library
lib	2014-02-27	Alper Kucukural	[d57e8f] chrom.sizes part in wigToBigWig fixed
scripts	2013-06-02	Alper Kucukural	[f88b4b] The error messages in cat and ls are corrected
README.txt	2013-05-15	hakan	[8d6099] Merge branch 'master' of ssh://git.code.sf.net/...

Read Me

#########################################################################
###################### A S P e a k    V e r s i o n   2 . 0 #############
#########################################################################




CONTENTS:
1) DESCRIPTION
2) REQUIREMENTS
3) RUNNING ASPEAK


Note: More detailed information is available in the user manual that comes with ASPeak.

1) DESCRIPTION

ASPeak is a free command-line software tool for finding clusters (peaks) in CLIP- / RIP- Seq data. 
It is implemented in Perl.
ASPeak uses an abundance sensitive peak detection algorithm to detect clusters (peaks)
of RNA-binding protein (RBP) sites in CLIP- / RIP- Seq data at nucleotide resolution.
ASPeak takes CLIP- / RIP- Seq, RNA-Seq and genome annotation data as input 
and it outputs peaks, namely RBP binding sites. 
Also, when control data is provided, ASPeak outputs the false discovery rates of the found peaks.



2) REQUIREMENTS

a) ASPeak is designed to run on Unix clones. It has been tested on Linux (Mint, Fedora, Ubuntu
and CentOS) and OS X. Users of other operating systems can install VirtualBox, freely available
at https://www.virtualbox.org, and install and run a Linux distribution virtually.
Perl comes with many Unix clones out of the box. ASPeak can run on Perl 5.8.8 or any later
version. To learn the Perl version installed in your system, in the terminal run the command
    
	 perl -v

b) The only non-standard perl module required to run ASPeak is Math::CDF. 
This module can be installed via CPAN

	 cpan -i Math::CDF

You can verify the installation of Math::CDF by
	
	perl -e "require Math::CDF"

The module is properly installed if there are no error messages.

c) If your input is in BAM, SAM or BOWTIE format, you need 
	SAMTools (available at http://samtools.sourceforge.net/ ) and 
	BEDTools available at http://code.google.com/p/bedtools/) 
installed in your system.

d) ASPeak requires wigToBigWig for file conversion from bedGraph to BigWig. 
You can obtain it from the appropriate directory at http://hgdownload.cse.ucsc.edu/admin/exe/



3) RUNNING ASPEAK

i) Extract the tar.gz file

	tar -xvf ASPeak.tar.gz

The executable scripts are in the scripts folder.
The main script is ASPeak.pl.
To see help, type

	./scripts/ASPeak.pl -help

ii) You can test ASPeak on the sample data that comes with it.

	./scripts/ASPeak.pl -lib example/RIPSeq/sampleRIPSeq.bowtie \
	-beddir example/annotation -rnaseq example/RNASeq/sampleRNASeq.bowtie \
	-control example/control/sampleControl.bowtie -outdir exampleOut

You can see the found peaks by
	
	more exampleOut/foundpeaks/sampleRIPSeq/peaks/sampleRIPSeq.peaks


iii) Prepare your data:

Accepted CLIP- / RIP- Seq, RNA-Seq and Control formats are
	i)   BAM
	ii)  SAM
	iii) BED
	iv)  BOWTIE

Annotation data must be in BED format.
You can obtain annotation data on the UCSC Genome Bioinformatics Site at http://genome.ucsc.edu/


You can run ASPeak on your CLIP-/RIP-Seq and RNA-Seq data by

	./scripts/ASPeak.pl -beddir annotation_directory -lib CLIP_RIP-Seq_file -rnaseq RNASeq_File -outdir output_directory 

The output files will be in the directory output_directory/foundpeaks

If, additionally, you have a control library, you can give it as input to see the false discovery rates

	./scripts/ASPeak.pl -beddir annotation_directory -lib CLIP_RIP-Seq_file -rnaseq RNASeq_File -outdir output_directory -control control_library_file

For other command line arguments of ASPeak, refer to the user manual or the plain old documentation via

		./scripts/ASPeak.pl -help