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Each step above can be done with commands below
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module load samtools samtools view -bS <samfile> > <bamfile>
samtools sort <bamfile> <prefix of sorted bamfile>
samtools index <sorted bamfile>
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| title | Copy a an exercise SAM file to your SCRATCH directory |
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cds
mkdir samtools_exercise
cd samtools_exercise
cp /corral-repl/utexas/BioITeam/core_ngs_tools/yeast_stuff/yeast_chip.sam .
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| Expand |
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| Code Block |
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module load samtools
samtools view -bS yeast_chip.sam > yeast_chip.bam
samtools sort yeast_chip.bam yeast_chip_sort
samtools index yeast_chip_sort.bam
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