isomiR tools - benchmark supportive scripts

The available scripts can be used to simulate sequencing reads with a mature microRNA dataset as reference, taking the individual lengths into account. Furthermore, one can simulate microRNA isoforms, using a reference mature microRNA dataset.

With the other scripts, one can evaluate the performance (TP,FP,FN) of isomiRID, isomiR-SEA and miraligner.

If you find the scripts useful, please cite:

Simulating small RNA sequencing runs

The script create_sequencing.pl can be used to simulate a microRNA sequencing run.

Dependencies :

ART

Installation :

Since it is a pure perl file, no installation is needed. Tested on Linux.

Usage :

./create_sequencing.pl

Details :

• The standard path of ART is specified as /opt/art_bin_MountRainier/art_illumina for illumina sequencing. If you whish to change the path or switch to another sequencing platform, you need to change the path at the beginnging of the source code
• The script is designed in a way that it only creates sequenced reads for microRNAs within a length between 17 and 30nt. If this does not fit your experimental design, you can change the array
  @mir_len = (17,18,19,20,21,22,23,24,25,26,27,28,29,30);
  by the lengths you may need or focus on.

Simulating microRNA isoforms (isomiRs)

The script create_isomiRs.pl is designed to simulate equally distributed microRNA isoforms.

• 5' template additions (1-3)
• 5' deletions (1-3)
• 3' template additions (1-3)
• 3' deletions (1-3)
• 3' non-template additions (1-3)
• SNPs in seed region
• SNPs outside of seed region

Dependencies :

none

Installation :

Since it is a pure perl file, no installation is needed. Tested on Linux.

Usage :

./create_isomiRs.pl <mature_mirs.fasta> <hairpin_mirs.fasta>
<mature_mirs.fasta> := The mature microRNA set of your species of interest
<hairpin_mirs.fasta> := The hairpin microRNA set of your species of interst

Output :

output file	description
mature_mirs.fasta-FIVE_ADD.fa	template 5' additions (1-3nt)
mature_mirs.fasta-THREE_ADD.fa	template 3' additions (1-3nt)
mature_mirs.fasta-THREE_DEL.fa	terminal 3' deletions (1-3nt)
mature_mirs.fasta-FIVE_DEL.fa	terminal 5' deletions (1-3nt)
mature_mirs.fasta-SNP_SEED.fa	SNPs in seed region (1-8)
mature_mirs.fasta-SNP_REST.fa	SNPs outside the seed region (9-end)
mature_mirs.fasta-NON_TEMPLATE.fa	non-template 3' additions (1-3nt)

Evaluate isomiR mining tools

Tool 1: eval_isomiRID_0.3.pl

Tool 2: eval_miraligner_0.3.pl

Tool 3: eval_isomiR-SEA_0.3.pl

All scripts come without warranty.