User Tools

Site Tools


bowtie2

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
bowtie2 [2017/10/10 17:45]
jokinsey Fixes the computation in the PBS script to fun in /scratch
bowtie2 [2017/10/10 17:47] (current)
jokinsey
Line 50: Line 50:
 </​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 ''​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. ​
  
-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''​. Then the output lambda_virus index files and the alignment results stored in the ''​eg1.sam''​ file, are moved to the ''​$PBS_O_WORKDIR''​ directory where the job was submitted from.
  
 Submit the job to the queue. Submit the job to the queue.
bowtie2.txt · Last modified: 2017/10/10 17:47 by jokinsey