Software Scripts and console applications MirMod

MirMod

Author: Marta Danch

MirMod is a bash script which execute consecutive commands launching cutadapt, bowtie2 and R scripts, which allow precise miRNA isoform expression levels estimation. Using MirMod one could detect all miRNA isoforms in analyzed samples, count it, indicate origin and references. 

MirMod script assigns to each isoform in each sample a miRNA reference name and one of four different attributes - type of isoform:

  • miRNA - an exact miRNA sequence
  • hairpin - an exact hairpin sequence
  • hairpin+mod - an exact miRNA sequence with additional modification at 3' end
  • hairpin+N1 - an miRNA or hairpin sequence with mismatches

MirMod script produces also other files with detected miRNA sequences, divided into different origin classes in each file, which may be used for further analysis.

MirMod as a final results produces four isoforms tables:

  • "ALL_izof.txt" - containing count table for all isoforms in all samples
  • "ALL_PROC_izof.txt" - containing percentage table for all isoforms in all samples
  • "ALL_filtr_izof.txt" - containing count table for isoforms with higher number of occurrences than "threshold" at least in one sample
  • "ALL_filtr_PROC_izof.txt" - containing percentage table for isoforms with higher number of occurrences than "threshold" at least in one sample 

The MirMod algorithm automates and simplifies analysis of miRNA data. Mapping the sequence to the various references, allows to distinguish probable origin of miRNA isoforms detected in samples and assigns them to different groups. User friendly output data form is prepared for further analysis, such as data classification. Another advantage is multi-threaded design of algorithm what makes it much more efficient.

More information about usage and dependencies in README file attached to MirMod archive.

 

Citation:
 
Danch M, Borys D, Stokowy T, Krohn K, Fujarewicz K: microRNA 3’-end Modification Detection Algorithm and Its Usage Example for Tissue Classification, Information Technologies in Biomedicine, Volume 3,  2014,   pp 285-294

 

Bash/R scripts: