cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.
cutadapt was developed by Marcel Martin. cutadapt website.
Set up a batch script along the following lines:
#!/bin/bash # this file is called job.bat cd /data/mydir module load cutadapt cutadapt -a AACCGGTT input.fastq > output.fastq
Submit this job with:
qsub -l nodes=1 job.bat
Set up a swarm command file along the following lines:
cd /data/user/mydir; cutadapt -a AACCGGTT input1.fastq > output1.fastq cd /data/user/mydir; cutadapt -a AACCGGTT input2.fastq > output2.fastq cd /data/user/mydir; cutadapt -a AACCGGTT input3.fastq > output3.fastq [...]
Submit this swarm with:
swarm -f swarm.cmd --module cutadapt
Most programs on the Biowulf cluster should be run as batch or swarm jobs, but users may occasionally want to run an interactive job for debugging purposes. Allocate an interactive node and run cutadapt there. Example:
biowulf% qsub -I -l nodes=1 qsub: waiting for job 2236960.biobos to start qsub: job 2236960.biobos ready p24% module load cutadapt p24% cd /data/user/mydir p24% cutadapt -a AACCGGTT input.fastq > output.fastq p24% exit biowulf%