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mkatari-bioinformatics-august-2013-igvnotes [2014/05/21 12:56] – created mkatarimkatari-bioinformatics-august-2013-igvnotes [2014/05/21 12:57] mkatari
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 3) For each sam files, convert to bam file 3) For each sam files, convert to bam file
 <code> <code>
-/export/apps/samtools/latest/bin/samtools view -S -b /home/ndegwa/manny_wkshop/cassava/bowtie_out/NDL06-132.sam > NDL06-132.bam+samtools view -S -b /home/ndegwa/manny_wkshop/cassava/bowtie_out/NDL06-132.sam > NDL06-132.bam
 </code> </code>
  
 4) sort each bam file 4) sort each bam file
 <code> <code>
-/export/apps/samtools/latest/bin/samtools sort NDL06-132.bam NDL06-132.bam.sorted+samtools sort NDL06-132.bam NDL06-132.bam.sorted
 </code> </code>
  
mkatari-bioinformatics-august-2013-igvnotes.txt · Last modified: 2014/05/21 13:45 by mkatari