riboSeqPipeline

RiboSeq pipeline

Installation

ln -s /mnt/picea/projects/aspseq/jhanson/riboseq-pipeline data
ln -s /mnt/picea/storage/reference .

Setup

SortMeRNA

To add SortMeRNA custom databases, do the following:

1. if needed (if there are many sequences), cluster them using cd-hit-est

cd-hit-est -i tRNA.fasta -o tRNA-id90.fasta

2. index it as a SortMeRNA database

module load bioinfo-tools SortMeRNA
indexdb_rna -L 10 --ref /mnt/picea/storage/reference/rRNA/sortmerna/v2.1/tRNA-id90.fasta,/mnt/picea/storage/reference/rRNA/sortmerna/v2.1/automata/tRNA-id90