User Tools

Site Tools


mkatari-bioinformatics-august-2013-igvnotes

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Next revision
Previous revision
mkatari-bioinformatics-august-2013-igvnotes [2014/05/21 12:56] – created mkatarimkatari-bioinformatics-august-2013-igvnotes [2014/05/21 13:45] (current) mkatari
Line 17: Line 17:
 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 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>
  
 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.1400676989.txt.gz · Last modified: 2014/05/21 12:56 by mkatari