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We've done this several times before, so you should be able to come up with the full command lines if you refer back to the original lesson.
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Be careful we are now mapping single-end reads, so you may have to look at the bowtie help to figure out how to do that! |
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| Please take me through all of the steps... |
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| Please take me through all of the steps... |
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module load bowtie
bowtie-build NC_017544.1.fasta NC_017544.1
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Now create a bowtie_commands file that looks like this using nano or another text editor: | Code Block |
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bowtie -p 3 -S NC_017544.1 SRR034450.fastq -S SRR034450.sam
bowtie -p 3 -S NC_017544.1 SRR034451.fastq -S SRR034451.sam
bowtie -p 3 -S NC_017544.1 SRR034452.fastq -S SRR034452.sam
bowtie -p 3 -S NC_017544.1 SRR034453.fastq -S SRR034453.sam
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Remember that there are 12 processors per node on Lonestar, so we choose to use 3 for each of the 4 jobs with the -p 3 option. Create the launcher script and run it: | Warning |
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Remember that you cannot qsub from within an idev shell! |
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module load python
launcher_creator.py -n bowtie -q development -cj bowtie_commands -t 0:30:00
qsub bowtie.sge
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