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Rilseq on NIH HPC Systems

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. RILseq is described in Melamed et al, Molecular Cell 63 (2016), pp. 884-897 (http://www.cell.com/molecular-cell/fulltext/S1097-2765(16)30413-0). 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.

Batch job on Biowulf

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

#!/bin/bash
module load rilseq

cd /data/$USER/dir
rilseq command
......

Then submit the file on biowulf

biowulf> $ sbatch script.sh

For more information regarding sbatch command : https://hpc.nih.gov/docs/userguide.html#submit

Swarm of Jobs on Biowulf

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

# this file is called script.swarm
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 script.swarm --module rilseq

For more information regarding swarm: https://hpc.nih.gov/apps/swarm.html#usage

Interactive job on Biowulf

Allocate an interactive session. Sample session:

[biowulf ~]$ sinteractive --mem=5g
salloc.exe: Pending job allocation 15194042
salloc.exe: job 15194042 queued and waiting for resources
salloc.exe: job 15194042 has been allocated resources
salloc.exe: Granted job allocation 15194042
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn1719 are ready for job

[cn1719 ~]$ module load rilseq

[cn1719 ~]$ rilseq command
Documentation
https://github.com/asafpr/RILseq