ADmiRE- Annotative Database of miRNA Elements

Published:

Oak, N. , Ghosh, R. , Huang, K. , Wheeler, D. A., Ding, L. and Plon, S. E. (2018), Framework for microRNA variant annotation and prioritization using human population and disease datasets. Human Mutation. Accepted Author Manuscript. doi:10.1002/humu.23668

https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.23668

Please reach out to me if you have any trouble using ADmiRE. This is my first attempt of making the code open access and I would love to keep improving my skills of making the code user-friendly. Afterall, we are all learning in the process...

Types of Input files

1. Tab-separated Files (*.tsv, *.mafplus, etc.): Using Perl script in the ./ADmiRE/ directory

2. VCF Files:

   • Using Ensembl Variant Effect Predictor (VEP) tool:

     Follow instructions in ./ADmiRE/annotate_VCF_using_VEP/Readme.md

     Requires prior VEP installation, suitable for users with existing VEP workflows.

   • Using ANNOVAR:

     ADmiRE is available as 'User-contributed-dataset' on ANNOVAR website for integration into existing pipelines.

     http://annovar.openbioinformatics.org/en/latest/user-guide/download/#user-contributed-datasets

Step-by-step Usage Guide

To annotate a Tab separated file:

1. Clone the ADmiRE repository

   git clone https://github.com/nroak/ADmiRE.git

   Alternatively, you can download the ADmiRE directory in a ZIP file format. Make sure to save this file as "ADmiRE" and NOT "ADmiRE-master". unzip ADmiRE.zip

2. Unzip the ADmiRE.tab.gz file (Unzipped file size ~232 MB)

   gzip -d ADmiRE.tab.gz

3. Run the script to annotate the input file in a tab separated format. Note: The script assumes header line to start with # or CHROM or Hugo_Symbol. If one of these first column headers are present, ADmiRE column names are added to the header line at the end of original header. Otherwise, the output file will not contain a header line.

   perl annotate_admire.pl [--input INPUT_FILE] [--output OUTPUT_FILE] [--admire_path PATH] [--chr NUMBER] [--pos NUMBER]

Detailed desription of the input options:

perl annotate_admire.pl [--input INPUT_FILE] [--output OUTPUT_FILE] [--admire_path PATH] [--chr NUMBER] [--pos NUMBER]

--input: INPUT_FILE [REQUIRED]

--output: OUTPUT_FILE (Default: INPUT_FILE.ADmiRE.tab) [OPTIONAL]

--admire_path: Path to ADmiRE.tab database. (Default: same directory with annotate_admire.pl) [OPTIONAL]

--chr: Column number in the INPUT_FILE with chromosome information. (Default: 1 -1st column) [OPTIONAL]

--pos: Column number in the INPUT_FILE with base position information. (Default: 2 -2nd column) [OPTIONAL]

To test your command is working:

Test files are provided for this Perl script. Please run,

perl annotate_admire.pl --input test_input.tab --output test_input.admire.tab