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Old Version 13

changes.mady.by.user Amelia W Hall

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New Version 14

changes.mady.by.user Daechan Park

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titlesolution
Code Block
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

 

Sorting takes quite big memory and long time. In order to save time, copy the results.

Code Block
titleCATCH UP
cp /corral-repl/utexas/BioITeam/core_ngs_tools/yeast_stuff/yeast_chip_sort.bam .
cp /corral-repl/utexas/BioITeam/core_ngs_tools/yeast_stuff/yeast_chip_sort.bam.bai .

Basic mapping stats

Code Block
samtools flagstat <bamfile>

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