How to use miARmaSeq

In order to execute miARma-Seq, a configuration file in INI format is mandatory. This file should contain information about your experiment's setup. The general information section must in the heading [General] at the beginning of the configuration file. Although the general section is required for each analysis with miARma-Seq, a configuration file containing only this section, but missing remaining parameters will not be suffcient to perform any analysis. So, please make sure you check for this.
Below you will find different configuration files to run pipeline in order to analyse RNA-Seq from raw "fastq" files. First it perfoms a quality analysis, then performs a trimming step, followed by an alignment process, and a summarization step to count mapped reads for each genomic feature. Next it runs a differential expression analysis, and finally conducts miRNA-mRNA target prediction. Each section has different parameters that can be adjusted according to your particular experimental setup and needs. We encourage you to refer the complete guide in the documentation page or use our examples in the next page.