Isomirage is a desktop application that counts the number of occurrences of small RNA molecules in a Bowtie .map alignment file.

FASTQ data of a small RNA sequencing experiment must be trimmed to remove adapter sequences and aligned to custom sequence libraries listing all isoforms of small RNA molecules.

Alignment of trimmed FASTQ data should be performed using Bowtie with --best and -v 0 switches and saved in .map output format.

Here is an example: /path_to_bowtie/bowtie /home/hmuller/mirna/mmu21/mmu21 --best -v 0 -q /home/user/mirna/sample_trimmed.fastq /home/user/mirna/sample.map

To build the custom library bowtie indices use: /path_to_bowtie/bowtie-build /home/user/mirna/mmu21/mmu21.fasta mmu21

Isomirage requires .map Bowtie alignments and a .genome file listing all isoforms as input.

Isomirage counts the number of occurrences in the .map file of each isoform listed in the .genome file and normalizes the counts using RMA and RPKM normalizations.

The output of Isomirage is a normalized matrix of isoform counts that can be used for follow-up analyses such as cluster analysis, for example.

Isomirage is written in the Java programming language and has been tested on Windows 7 and MacOS 10 operating systems.