This file contains a brief description of the motif analysis pipeline of PARAlyzer 
interaction sites for:
1. de-novo motif discovery: in case of sequence-specific RBPs (cERMIT version 1.1)
2. microRNA enrichment analysis: in case of AGO PAR-CLIP (mEAT veresion 1.0)
Basic instructions on how to run the code are also included.
Example input files are provided along with Ruby pre-processing scripts and binary executables
- Pumilio2 human PAR-CLIP dataset  (Hafner et al. 2010)
- Quaking human PAR-CLIP dataset   (Hafner et al. 2010)
- IG2BP1 human PAR-CLIP dataset    (Hafner et al. 2010)
- Argonaute human PAR-CLIP dataset (Hafner et al. 2010)

NB: using the symbol '#' to indicate a 'comment'

Input files
===========
# output file from the PARalyzer analysis
data/<RBP_name>.csv

# parameter file specifying the covariates to include in the linear regression as part of the mEAT analysis
# (comments are added explaining each parameter type)
params/covariates.params

# file, containing specific paramters for the analysis of <RBP_name>
# (comments are added explaining each parameter type)
params/<RBP_name>.params

Output file
===========
# results from the mEAT/cERMIT analysis of the PARalyzer interaction sites
data/<RBP_name>

Executable script
=================
# runs pre-processing of the PARalyzer output
# followed by motif analysis using mEAT or cERMIT 

# run pre-processing and motif analysis of all datasets described in the paper
option 1
--------
./do_all

# run pre-processing and motif analysis as separate scripts for individual RBPs
option 2
--------
./pre_process_<RBP_name>
./run_<RPB_name>_analysis

Running with default settings
=============================
In order to analyse a new dataset produced by PARalyzer using the default analysis options,
the input files for the existing RBPs can be used as TEMPLATES. In more detail:

1. ensure the PARalyzer output file is named 'data/<RBP_name>.csv'
2. create new 'params/<RBP_name>.params' copying the contents of 'params/QKI_EbR_5deep.params'
and replacing the name 'QKI_EbR_5deep' with <RBP_name>
3. create new 'pre_process_<RBP_name>' and 'run_<RPB_name>_analysis' files copying the 
contents of 'pre_process_QKI_EbR_5deep' and 'run_QKI_EbR_5deep_analysis', replacing the 'QKI_EbR_5deep' with <RBP_name>

NB: If mEAT analysis is to be performed use the 'AGO_EbR_5deep' input files as a TEMPLATE instead of 'QKI_EbR_5deep'



