Initialize

Prepare directories¶

Create a working directory and subdirectories:

mkdir ISOMIR
cd ISOMIR
mkdir fastq_files

Index¶

You will need an Index directory for mapping to rRNA, tRNA, snoRNA, miRNA, transcriptome, and mycoplasma. You can download this Index for hg38. Extract the downloaded directory :

tar zxvf index.tar.gz

Scripts¶

Download the following files in the working directory:

• isomiR.nf
• isomiR.sh
• nextflow.config
• motif-consensus.fa