sRNAnalyzer
===========
sRNAnalyzer is a flexible and customizable pipeline for the analysis of
small RNA sequencing data.

See the GettingStarted.md file for instructions for installing and configuring
the pipeline. Here's an example of a typical use case involving analysis of human
small RNA sequencing data.

Here is the pipeline_config.yaml configuration file for this analysis,

    preprocess:
        kit:        NEB
        gzip:       true
        stop-oligo: false
    
    alignment:
        type: single
        human_miRNA:     2
        human_miRNA_sub: 2
        human_piRNA:     2
        human_snoRNA:    2

There is also the database configuration file that needs to be
setup properly. For instructions, see GettingStarted.md.
To learn more about the configuration files, see ConfigDocs.md.

The commands for the analysis are,
    
    preprocess.pl --config pipeline_config.yaml
    align.pl /home/data pipeline_config.yaml DB_config.conf
    summarize.pl DB_config.conf --project my_project

This will produce summarized profile and feature files with read counts
which can be used for further analysis, such as differential expression.