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mkatari-bioinformatics-august-2013-igvnotes [2014/05/21 15:57]
mkatari
mkatari-bioinformatics-august-2013-igvnotes [2014/05/21 16:45] (current)
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>​
-samtools view -S -b /​home/​ndegwa/​manny_wkshop/​cassava/​bowtie_out/​NDL06-132.sam > NDL06-132.bam+samtools view -S -b NDL06-132.sam > NDL06-132.bam
 </​code>​ </​code>​
  
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 5) create index for each bam file 5) create index for each bam file
 <​code>​ <​code>​
-/​export/​apps/​samtools/​latest/​bin/​samtools index NDL06-132.bam.sorted.bam+samtools index NDL06-132.bam.sorted.bam
 </​code>​ </​code>​
  
  
mkatari-bioinformatics-august-2013-igvnotes.txt · Last modified: 2014/05/21 16:45 by mkatari