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bowtie2 [2017/09/28 18:00]
jokinsey created
bowtie2 [2017/10/10 17:45]
jokinsey Fixes the computation in the PBS script to fun in /scratch
Line 30: Line 30:
  
 <​code>​ <​code>​
-#/!/bin/bash+#!/bin/bash
 #PBS -q tiny12core #PBS -q tiny12core
 #PBS -N bowtie2 #PBS -N bowtie2
 +#PBS -l nodes=1:​ppn=12
 #PBS -j oe #PBS -j oe
 #PBS -m abe #PBS -m abe
 #PBS -M jokinsey@uark.edu #PBS -M jokinsey@uark.edu
-#PBS -l nodes=1:​ppn=12 
 #PBS -l walltime=00:​05:​00 #PBS -l walltime=00:​05:​00
  
 cd $PBS_O_WORKDIR cd $PBS_O_WORKDIR
 +cp lambda_virus.fa /​scratch/​$PBS_JOBID
 +cp reads_1.fq /​scratch/​$PBS_JOBID
 +cd /​scratch/​$PBS_JOBID
  
 bowtie2-build lambda_virus.fa lambda_virus bowtie2-build lambda_virus.fa lambda_virus
 bowtie2 -x lambda_virus -U reads_1.fq -S eg1.sam bowtie2 -x lambda_virus -U reads_1.fq -S eg1.sam
 +
 +mv lambda_virus* eg1.sam $PBS_O_WORKDIR/​
 </​code>​ </​code>​
 +
 +The ''​PBS''​ script above copies the unindexed ''​FASTA''​ file for the lambda virus and the ''​FASTAQ''​ file containing the unpaired reads for the lambda phage to the ''/​scratch/​$PBS_JOBID''​ directory where we will run the computation. Then it copies the output lambda_virus index files and the alignment results stored in the ''​eg1.sam''​ file, back to the ''​$PBS_O_WORKDIR''​ directory where the job was submitted from.
  
 The ''​bowtie2-build''​ line will output files that represent the index for the Lambda phage reference genome. The line below that runs the bowtie2 aligner, and outputs the alginments to a ''​SAM''​ file called ''​eg1.sam''​. The ''​bowtie2-build''​ line will output files that represent the index for the Lambda phage reference genome. The line below that runs the bowtie2 aligner, and outputs the alginments to a ''​SAM''​ file called ''​eg1.sam''​.
bowtie2.txt · Last modified: 2017/10/10 17:47 by jokinsey