====Kallisto====

Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. More information on kallisto can be found [[https://pachterlab.github.io/kallisto/|here]]

====Enviornment Setup====

Edit your ''$HOME/.bashrc'' file to include the load command below for kallisto. You will have to log back in for this to take effect.

<code>
module load kallisto
</code>

In your ''$HOME'' directory create the directory ''KALLISTO-JOBS'' where we will submit jobs to the queue. Inside that directory copy the 'test' directory from where kallisto is located.

<code>
razor-l1:jokinsey:~$ mkdir KALLISTO-JOBS
razor-l1:jokinsey:~$ cd KALLISTO-JOBS/
razor-l1:jokinsey:~/KALLISTO-JOBS$ cp -r share/apps/bioinformatics/kallisto/kallisto_linux-v0.43.1/test/ .
</code>

Now we can write the script to run out test job.

====Example Job====

Inside the ''$HOME/KALLISTO-JOBS/test'' create a ''PBS'' script with the information below to run our example job.

<code>
#!/bin/bash
#PBS -N kallisto
#PBS -q tiny12core
#PBS -j oe
#PBS -o kallisto.$PBS_JOBID
#PBS -l nodes=1:ppn=12
#PBS -l walltime=1:00:00
#PBS -M jokinsey@email.uark.edu

cd $PBS_O_WORKDIR
cp {transcripts.fasta.gz,reads_1.fastq.gz,reads_2.fastq.gz} /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID

kallisto index -i transcripts.idx transcripts.fasta.gz
kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz

cp -r output $PBS_O_WORKDIR/output.$PBS_JOBID
</code>

The script above first goes to the directory we submitted the job from, then it copies the files that are needed to ''/scratch/$PBS_JOBID'' the directory where we will be running out job and it moves to that directory. Using kallisto it builds an index from the ''transcripts.fasta.gz'' file. Next it quantifies the number of abundances of the transcripts using the two read files. The output will be in the directory ''output'' which we move to the submitted directory and append the ''$PBS_JOBID'' so it is unique in case you want to run this job more than once.

All thats left is to submit the job.

<code>
razor-l1:jokinsey:~/KALLISTO-JOBS/test$ qsub kallisto.pbs
</code>

In the ''$HOME/KALLISTO-JOBS/test/output.$PBS_JOBID'' directory the most important output should be the ''abundance.tsv'' or ''abundance.txt'' file. More information on the output can be found [[https://pachterlab.github.io/kallisto/starting|here]]