Biowulf High Performance Computing at the NIH
CTK on Biowulf

Crosslinking and immunoprecipitation followed by highthroughput sequencing (HITS-CLIP or CLIP-Seq) has now been widely used to map protein-RNA interactions on a genome-wide scale. The CLIP Tool Kit (CTK) is a software package that provides a set of tools for analysis of CLIP data starting from the raw reads generated by the sequencer. It includes pipelines to filter and map reads, collapse PCR duplicates to obtain unique CLIP tags, define CLIP tag clusters and call peaks, and define the exact protein-RNA crosslink sites by CIMS and CITS analysis. This software package is an expanded version of our previous CIMS package.

Crosslinking induced mutation site (CIMS) and cross linking induced truncation site (CITS) analyses are computational methods for CLIP data analysis to determine the exact protein-RNA crosslink sites and thereby map protein-RNA interactions at single-nucleotide resolution. These methods are based on the observation that UV crosslinked amino-acid-RNA adducts can introduce reverse transcription errors, including mutations and premature in cDNAs at a certain frequency, which are captured by sequencing and subsequent comparison of CLIP tags with a reference genome.

References:

Shah,A., Qian,Y., Weyn-Vanhentenryck,S.M., Zhang,C. 2017. CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data. Bioinformatics. 33:566-567

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --mem=5g
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 ctk

[user@cn3144 ~]$ fastq_filter.pl in.fq out.fq 

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

Batch job
Most jobs should be run as batch jobs.

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

#!/bin/bash
set -e
module load ctk
cd /data/$USER
fastq_filter.pl in.fq out.fq

Submit this job using the Slurm sbatch command.

sbatch --mem=5g ctk.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

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

cd dir1; fastq_filter.pl in.fq out.fq
cd dir2; fastq_filter.pl in.fq out.fq
...
cd dir10; fastq_filter.pl in.fq out.fq

Submit this job using the swarm command.

swarm -f ctk.swarm -g 5 --module ctk
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module ctk Loads the ctk module for each subjob in the swarm