### Download data

	wget  ftp://.../<sra file>


### Convert from sra to fastq
	
	fastq-dump.2.3.2 <sra file>


### Create fasta index for IGV visualisation

	samtools faidx <fasta file>


### Align

	### create index 
		
	bowtie-build  $organism".fasta" index/$organism;
	!!! if you use a color index please see details on http://bowtie-bio.sourceforge.net/manual.shtml

	### align reads
	
	bowtie -S <organism_index> <reads.fastq> | samtools view -bS -o <aligned_reads.bam>
	(the above line joins the alignment and bam file creation commands)

	!!! pay attention to read trimming ( you can use homerTools to do the trimming)
	!!! see bowtie site for the color index


### Compute  read counts  

igvtools count -w 1 --postExtFactor 1 --strands read  <aligned_reads.bam>  <counts.wig file> <.chrom.sizes file>


### Compute  read counts  

igvtools count -w 1 --postExtFactor 1 --strands read  <aligned_reads.bam>  <counts.wig file> <.chrom.sizes file>


### Run Parseq_pmcmc

	!!! before you start  using Parseq make sure that you installed the GSL library
	!!! to run Parseq you need to have in a folder the fasta, chrom.sizes and counts files.We'll give an example for the Sacharomyces cerevisiae .
 	>> In a folder named "cerevisiae" create a subfolder  named "counts". 
	>> Copy in this  subfolder the "cerevisiae.fasta", "counts.wig" file (obtained using igvtools) and "cerevisiae.chrom.sizes" files.  
	>> Then you can execute Parseq_pmcmc

	Parseq_pmcmc <speed> <organism> <strand>  <chromosome> <data folder> <results folder> <parseq folder>
	
	!!! Example:
	data_folder="/home/xxx/cerevisiae/"; results_folder="/home/xxx/cerevisiae/results"; org="cerevisiae"; parseq_parameters_folder="/home/parseq/"; 
	Parseq_pmcmc fast $org + genome $data_folder $results_folder $parseq_parameters_folder

This command will execute Parseq on  the "+" chromosome  using the "/home/xxx/cerevisiae/counts/counts.wig" counts file, "/home/xxx/cerevisiae/counts/cerevisiae.chrom.sizes" and "/home/xxx/cerevisiae/counts/cerevisiae.fasta"  fasta file.

Parseq_pmcmc works in two steps:

	1) It will compute read count distribution parameters and will create:
		1.1) a parameter file "Parameters_initial" in the "/home/xxx/cerevisiae/counts/" folder
		1.2) ORF regions file sfor each chromosome
		1.3)

	2) An output folder "/home/xxx/cerevisiae/results"  where results will be written:
		2.1) Particles  were each line represents a transcription profile sample;
		2.2) Particles_struct  - each line is a local bias profile sample
		2.3) Breakpoints - each line is a breakpoints profile sample


From these  samples you can  compute the expected transcription profile and estimate the transcrition boundaries:

### Run Parseq_particle2proba 

	Parseq_particle2proba <expression_threshold> <organism> <strand>  <chromosome> <data_folder> <results_folder> [score penalty]

	!!! Example:
	Parseq_particle2proba 0.1 cerevisiae "+" genome $data_folder $results_folder

Parseq_particle2proba  will produce:
	
	1) Expression level estimation
	2) Transcription probability profile
	3) Breakpoints estimates.