Post date: May 13, 2014 10:10:47 PM
#We need to change the format from sam to bam, a compressed version of sam, and then we need to sort the bam files. See wrap_qsub_rc_sam2bam.pl. I changed "pbs.llucas" and the directory my sam files are in. On the USU cluster:
perl wrap_qsub_rc_sam2bam.pl alnE-SM-*sam
#Here's an example of the commands being submitted:
cd /labs/evolution/projects/nana/
samtools view -b -S -o alnE-SM-W-HO-263.bam alnE-SM-W-HO-263.sam
samtools sort alnE-SM-W-HO-263.bam alnE-SM-W-HO-263.sorted
samtools index alnE-SM-W-HO-263.sorted.bam
#Job #s: 254950-255144.torque. These should take about a day.
#May 15: 6 jobs got stuck or something, so we killed them and combined them into one short run. They finished in 13 seconds.