This package can be used to analyzed RILseq experiments. It is written for a prokaryotic genome, without splice junction mapping and with some additional features. The package handles the different stages processing fastq files to pairs of interacting RNAs and some statistics. It does not handle quality issues, adapter removing etc. so the fastq files should be treated with cutadapt or equivalent before applying this package.

References:

• http://www.cell.com/molecular-cell/fulltext/S1097-2765(16)30413-0

• https://github.com/asafpr/RILseq

• Module Name: rilseq (see the modules page for more information)

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load rilseq
[user@cn3144 ~]$ rilseq command

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
set -e
module load rilseq
rilseq command

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] batch.sh

Create a swarmfile (e.g. job.swarm). For example:

cd dir1;rilseq command 1; rilseq command 2
cd dir2;rilseq command 1; rilseq command 2
cd dir3;rilseq command 1; rilseq command 2

Submit this job using the swarm command.

swarm -f job.swarm [-t #] --module rilseq