See wiki at https://pbtech-vc.med.cornell.edu/git/mason-lab/meripper/wikis/home for usage. 

== Installation Instructions
MeRIPPeR is compatible with Linux and Mac. 
Download MeRIPPeR here: http://sourceforge.net/projects/meripper/

=== Other software dependencies
* Java (>= version 7)
* R   
* Perl  
* STAR  
* BWA  
* TopHat  
* SAMtools  
* bedtools  
* bedGraphToBigWig  

==== R package dependencies
* getopt  
* zoo

=== Reference files needed
* Genome: FASTA, FASTA index, BWA index, TopHat index, STAR index  
* RefSeq annotation files

********************************************************************************************
***************************************MANUAL***********************************************
********************************************************************************************

== Set up

Ensure all sequence files are in the directory from which MeRIPPeR is to be run (otherwise STAR will fail to find files)

== Create Makefile 

=== Configuration XML 

==== XML Structure 
  <pre><nowiki>
  <meripper>
    <data>
        <samples>
            <sample name="sample_name">
                <replicate name="replicate_name">
                    <ip>ip_name</ip>
                    <control>control_name</control>
                </replicate>
            </sample>
        </samples>
    </data>
    <configuration>
        <'configuration variable'>
        </'configuration variable'>
    </configuration>
  </meripper> 
  </nowiki>
  </pre>

* IP/control names must match file names. Do not include ".fastq.gz"

==== Possible XML <configuration> variables 

  * aligner - Choose STAR or TopHat for alignment
  * num_threads - Number of threads to use
  * genome - Genome name
  * genome_fa - Path to FASTA file of genome
  * genome_fai - Path to .fai file of genome
  * genome_dir - Path to directory of genomes
  * tophat_genome_dir - Path to TopHat reference genome directory
  * bwa_index - Path to BWA index
  * refseq_dir - Path to RefSeq annotation files
  * genome_sizes - Path to file of chromosome sizes
  * mapping_quality_threshold - Filter out reads with  quality less than this threshold
  * window_size - Window step size
  * window_min_size - Filter out windows smaller than this minimum size
  * window_max_size - Filter out windows bigger than this maximum size
  * alpha - p-value alpha threshold

=== XML to Makefile 
  <code>perl config.pl [config.xml] </code>
* Input: config.xml unless otherwise specified.  
* Output: Makefile



== Makefile targets 

=== make all
Pipeline that runs the equivalent of <code>make peaks</code>, <code>make peaks-annotate</code>, <code>make wc</code>.

=== make 
Defaults to <code>make peaks</code>.

=== make peaks 
* Input: <samples>.fasta.gz
  * Aligns samples
  * Calls peaks (<sample>*.peaks-split.bed)
  * Calls true negative peaks (TN_<sample>*.peaks-split.bed)
  * plots
* Output: <sample>*.peaks-split.bed, TN_<sample>*.peaks-split.bed, alignment output and logs.

=== make peaks-annotate
* Input: <samples>.fasta.gz
  * Aligns samples
  * Calls peaks (<sample>*.peaks*.bed)
  * Calls true negative peaks (TN_<sample>*.peaks-split.bed)
  * Plots occupancy of peaks across 3' UTR, CDS, and 5' UTR (<sample>*.tpp.n*.pdf)
* Output: <sample>*.tpp.n*.pdf, <sample>*.peaks-split.bed, TN_<sample>*.peaks-split.bed, alignment output and logs.

=== make bigwig 
* Input: <samples>.fasta.gz
  * Aligns samples
  * Converts <samples>.bam to <samples>.bedgraph
  * Converts <samples>.bedgraph to <samples>.bw
* Output: <samples>.bw, <samples>.bedgraph, alignment output and logs.

=== make refseq 
* Input: <samples>.fasta.gz
  * Aligns samples
  * Computes read counts (<samples>.rc.txt) and fraction of aligned reads (<samples>.frac.txt)
  * Calculates RPKM at RefSeq genes (<samples>.refseq.genes.rpkm.bed) and exons (<samples>.refseq.exons.rpkm.bed)
  * Computes library-wide library-size (<aligner>.library-size.txt), number of reads mapped (<aligner>.mapped.txt), read counts (<aligner>.read-counts.txt), and RPKM (<aligner>.rpkm.txt)
* Output: <samples>.refseq.genes.rpkm.bed, <samples>.refseq.exons.rpkm.bed, <samples>.rc.txt, <samples>.frac.txt, <aligner>.library-size.txt), <aligner>.mapped.txt, <aligner>.read-counts.txt, <aligner>.rpkm.txt, alignment output and logs.

=== make wc 
* Input: <samples>.fasta.gz
  * Aligns samples
  * Computes read counts (<samples>.rc.txt) and fraction of aligned reads (<samples>.frac.txt)
* Output: <samples>.rc.txt, <samples>.frac.txt, alignment output and logs.


== MeRIPPeR.jar options 
<code>
usage: MeRIPPER [-a <threshold>] -c <control-file> -g <genome-sizes> [-j <STAR Junctions file>] [-k <Minimum coverage>] -m <MeRIP-sample-file> [-n <minimum window size>] -o <output> [-p <BenjaminiHochberg|Bonferroni>] [-r <Bed 12 genes file>] [-s <step size>] [-t <# threads>] [-w <window size>]
</code>

 -a,--alpha <threshold>                           p-value alpha threshold
 -c,--control <control-file>                      control file
 -g,--genome-sizes <genome-sizes>                 Genome Chromosome Sizes
 -j,--junctions <STAR Junctions file>             splice junctions from
                                                  STAR
 -k,--junctions-min-coverage <Minimum coverage>
 -m,--merip <MeRIP-sample-file>                   MeRIP sample file
 -n,--min-window <minimum window size>            Filter out windows
                                                  smaller than the minimum
                                                  size
 -o,--output <output>                             output file
 -p,--p.adjust <BenjaminiHochberg|Bonferroni>     p-value adjustment
                                                  method
 -r,--genes <Bed 12 genes file>                   Genes annotation
                                                  (RefSeq)
 -s,--step-size <step size>                       Window Step Size
 -t,--num-threads <# threads>                     # of threads
 -w,--window-size <window size>                   Window Size

The necessary arguments are not in brackets, are:
 -c,--control <control-file>                      control file
 -g,--genome-sizes <genome-sizes>                 Genome Chromosome Sizes
 -m,--merip <MeRIP-sample-file>                   MeRIP sample file
 -o,--output <output>                             output file