miARmaSeq : miRNA And RNA Multiprocess Analysis.
Rocio Nuñez Torres, Eduardo Andrés-León & Ana M. Rojas.
It is a miRNASeq analysis workflow, which automatically performs several analysis processes using state-of-art software. It includes:
(a) Quality analysis of the reads (by FASTQ )
(b) Adapter removal using Cutadapt or Reaper software. If the adapter information is not available a computational prediction of the adapter sequence can be performed using Minion.
(c) Alignment to the reference genome (indexing is included within the pipeline) (by Bowtie1/2)
(d) Read quantification by desired feature (premiRNA, mature miRNA,...) using Htseq-Count.
(e) Quality analysis to determine the correlation among replicates using graphical approaches, such as PCA, MDS or hierarchical clustering
(f) Differential Expression Analysis (DEA) using EdgeR and/or NOISeq.
Our pipeline process standard sequencing files (fastq format) performing several and parallelized analysis resulting in a results file (in tsv format) with DEA features for each experimental condition evaluated and an additional quality report file.