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| Just give me the answer... |
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| Just give me the answer... |
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| Code Block |
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module load bowtie
bowtie-build NC_017544.1.fasta NC_017544.1
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Now create a commands file that looks like this: | 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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Create the launcher script and run it: | Code Block |
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module load python
launcher_creator.py -n bowtie -q development -c commands -t 0:30:00
qsub launcher.sge
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Convert
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Bowtie output to BAM
Edit your commands file so that you convert all of these files from SAM to sorted and indexed BAM.
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