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kallisto [2017/10/17 18:43] (current)
jokinsey Created Kallisto documentation
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 +====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]]
kallisto.txt · Last modified: 2017/10/17 18:43 by jokinsey