Salmon is a tool for transcript quantification from RNA-seq data. To use Salmon all you need is a FASTA
file containing your reference transcript, and a file or files containing your FASTA
/FASTAQ
reads. There are other files that can be used to run Salmon, documentation on this can be found here.
Edit your $HOME/.bashrc
file to include the load command for Salmon. You will have to log back in for this to take effect.
module load salmon/0.8.2
In your $HOME
directory create a directory SALMON-JOBS
where we will run the example job below, and copy the sample data provided from Salmon into this directory. Go into the $HOME/SALMON-JOBS
directory to unzip and open the tar file which will open the sample_data
directory.
razor-l3:jokinsey:~$ mkdir SALMON-JOBS razor-l3:jokinsey:~$ cp /share/apps/bioinformatics/salmon/Salmon-0.8.2_linux_x86_64/sample_data.tgz SALMON-JOBS/ razor-l3:jokinsey:~$ cd SALMON-JOBS/ razor-l3:jokinsey:~/SALMON-JOBS$ tar -xzf sample_data.tgz razor-l3:jokinsey:~/SALMON-JOBS$ cd sample_data
In the $HOME/SALMON-JOBS/sample_data
directory create a PBS
script to submit the job. The script should look like the on below.
#!/bin/bash #PBS -N salmon #PBS -q tiny12core #PBS -j oe #PBS -o salmon.$PBS_JOBID #PBS -l nodes=1:ppn=12 #PBS -l walltime=1:00:00 #PBS -M jokinsey@email.uark.edu cd $PBS_O_WORKDIR cp {reads_1.fastq,reads_2.fastq,transcripts.fasta} /scratch/$PBS_JOBID cd /scratch/$PBS_JOBID salmon index -t transcripts.fasta -i transcripts_index salmon quant -i transcripts_index -l IU -1 reads_1.fastq -2 reads_2.fastq -o out cp -r out $PBS_O_WORKDIR/out.$PBS_JOBID
The script above copies the files we will be working with the the directory we will be working in /scratch/$PBSJOBID
to the new output directory so that we make a unique directory. This ensures we don't copy into an already created directory if you wanted to run this script more than once.
, after that it creates an index from the
transcripts.fasta file. Then we run salmon with the index we just build and the reads from the sample date. The information will be in a directory called
out. Lastly we copy the directory to the directory we ran the job from, and append the
$PBSJOBID
All that left is to submit the job.
razor-l3:jokinsey:~/SALMON-JOBS/sample_data$ qsub salmon.pbs
In the $HOME/SALMON-JOBS/sampledata/out.$PBSJOBID/
directory which will have the output from the job the most important file is the quant.sf
file. More information on the output can be found here.