User Tools

Site Tools



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

Link to this comparison view

Both sides previous revision Previous revision
mkatari-bioinformatics-august-2013-igvnotes [2014/05/21 15:57]
mkatari-bioinformatics-august-2013-igvnotes [2014/05/21 16:45] (current)
Line 17: Line 17:
 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>​
Line 27: Line 27:
 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