## To install the package just type

perl install_quant.pl 

## and all necessary PATH variables should be set and third party software should be downloaded and installed
## in case of an installation error please open an issue in the github repository or sent an email
## to sd.mackowiak@gmail.com

## Once properly installed the tool can be directly run with preprocessed read files
## Optimally you supply one or more fasta files which have the following id line format
>abc_int_xINT

where 
      'abc' designates a sample id 
      'int' is a number that in combination with the sample id is unique in the whole file
	  'xINT' designates the abundance of the read sequence in your raw files.

## In case you have raw fastq files for example you can run 

preprocess.pl -a ADAPTER_sequence -f your_file.fastq.gz

or on multiple files 

preprocess.pl -a ADAPTER_sequence -f fastq.gz

## this will we expanded in do *.fastq.gz which designates all fastq.gz files in your directory

## the output files will be called *.collapsed.fa and will have the proper id lines already

## In case every distinct sequence in the fasta file ocurred only once then each id will have x1 in the third field
## However, since sequences usually occur more then once a raw sequencing file, eg. a sequence occurs 100 times,
## then the id line for this particular sequence will end with x100

typical usage cases for quantify

if not done yet download a precursor and mature miRNA sequence file by typing

perl get_mirbase.pl 21

## this will download mirbase 21 and save files to ~/mirbase/21/



