miARma

miARma is a fully customizable pipeline for NGS transcriptome analyses. Including gene/transcripts, miRNAs and circRNAs expression measurements. Created at Computational Biology and Bioinformatics Group (CbBio) Institute of Biomedicine of Seville. IBIS (Spain) Modified and Updated at Bioinformatics Unit at IPBLN-CSIC (Institue for Parasitology and Biomedicine Lopez-Neyra, CSIC). Granada (Spain). Copyright (c) 2017 IBIS & IPBLN. All rights reserved.

miARma 1.7.1 release (21/Aug/17)

Minor bugs fixed eg.

• No aligned reads in hisat2 paired end analysis added.

Added stuff:

• Unaligned files are compressed
• miRDeeparam added to include parameters to miRDeep execution

miARma 1.7.0 release (09/Aug/17)

• Hisat v2.1.0 has been included as a mRNA aligner.
• STAR v020201 has been included as a mRNA aligner.

1. Included in miARma

Quality Software

• Fastqc v0.11.5

Trimming Softare

• CutAdapt v1.9.1
• Minion v15-065
• Reaper v15-065

Aligners

• Bowtie v1.1.2
• Bowtie v2.2.8
• TopHat v2.1.1
• BWA v0.7.13
• Hisat v2.1.0
• STAR v020201

Entity Quantification####

• feactureCounts v1.5.0-p1
• Ciri v1.2
• Ciri v2.0.1
• miRDeep v2

Others

• RNAfold v2.2.4
• Samtools v1.3

2. Pre-requisites

miARma-Seq is a tool that provides an easy and common interface to various analysis software. It also intends to reduce to the minimum the number of dependencies. Nevertheless, some basic programs listed below must be correctly installed:

• Perl v5.6.0 or higher.
• Java JDK v.1.6. or higher.
• R environment v.3.2 or higher.
• Bioconductor v.1.3 or higher.

Compilers:

• Apple:
  • Xcode
• Linux:
  • Gcc
  • �make

How do I get set up?

• miARma can be installed using the following guide

Guidelines/How to

• miRNAs guide
• mRNAs guide
• circRNAs guide

Code Documentation

• Perldoc

Who do I talk to?

• [email protected]