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salmon [2017/10/17 17:41] (current)
jokinsey Created Salmon documentation
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 +====Salmon====
 +
 +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 [[http://​salmon.readthedocs.io/​en/​latest/​salmon.html|here]].
 +
 +====Enviornment Setup====
 +
 +Edit your ''​$HOME/​.bashrc''​ file to include the load command for Salmon. You will have to log back in for this to take effect.
 +
 +<​code>​
 +module load salmon/​0.8.2
 +</​code>​
 +
 +In your ''​$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 ''​$HOME/​SALMON-JOBS''​ directory to unzip and open the tar file which will open the ''​sample_data''​ directory.
 +
 +<​code>​
 +razor-l3:​jokinsey:​~$ 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
 +</​code>​
 +
 +====Example Job====
 +
 +In the ''​$HOME/​SALMON-JOBS/​sample_data''​ directory create a ''​PBS''​ script to submit the job. The script should look like the on below.
 +
 +<​code>​
 +#!/bin/bash
 +#PBS -N salmon
 +#PBS -q tiny12core
 +#PBS -j oe
 +#PBS -o salmon.$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
 +</​code>​
 +
 +The script above copies the files we will be working with the the directory we will be working in ''/​scratch/​$PBS_JOBID'',​ after that it creates an index from the ''​transcripts.fasta''​ file. Then we run salmon with the index we just build and the reads from the sample date. The information will be in a directory called ''​out''​. Lastly we copy the directory to the directory we ran the job from, and append the ''​$PBS_JOBID''​ 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.
 +
 +All that left is to submit the job.
 +
 +<​code>​
 +razor-l3:​jokinsey:​~/​SALMON-JOBS/​sample_data$ qsub salmon.pbs
 +</​code>​
 +
 +In the ''​$HOME/​SALMON-JOBS/​sample_data/​out.$PBS_JOBID/''​ 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 [[http://​salmon.readthedocs.io/​en/​latest/​file_formats.html|here]].
  
salmon.txt · Last modified: 2017/10/17 17:41 by jokinsey