#sh QSUB.mapsplice.sh 3D.1.control.1.txt 3D.1.control.2.txt 3D.1.control.102111 
#sh QSUB.mapsplice.sh 3D.2.control.1.txt 3D.2.control.2.txt 3D.2.control.102111
#sh QSUB.mapsplice.sh 3D.0.control.1.txt 3D.0.control.2.txt 3D.0.control.102111
#sh QSUB.mapsplice.sh 3D.0.sf2.1.txt 3D.0.sf2.2.txt 3D.0.sf2.102111
#sh QSUB.mapsplice.sh 2D.0.control.1.txt 2D.0.control.2.txt 2D.0.control.102111

#q_stat=$(qstat | awk '{print $5}' | grep q |wc -l)
#r_stat=$(qstat | awk '{print $5}' | grep r |wc -l)
#while ((($r_stat>0 )||($q_stat>0)))
#do
#        echo "qw:"$q_stat" r:"$r_stat
#        q_stat=$(qstat | awk '{print $5}' | grep q  |wc -l)
#        r_stat=$(qstat | awk '{print $5}' | grep r  |wc -l)
#        sleep 100
#done
#
#sh QSUB.mapsplice.sh 2D.0.sf2.1.txt 2D.0.sf2.2.txt 2D.0.sf2.102111
#q_stat=$(qstat | awk '{print $5}' | grep q |wc -l)
#r_stat=$(qstat | awk '{print $5}' | grep r |wc -l)
#while ((($r_stat>0 )||($q_stat>0)))
#do
#        echo "qw:"$q_stat" r:"$r_stat
#        q_stat=$(qstat | awk '{print $5}' | grep q  |wc -l)
#        r_stat=$(qstat | awk '{print $5}' | grep r  |wc -l)
#        sleep 100
#done



/data/zhang/makerman/MAP_TOOLS/cufflinks-1.1.0.Linux_x86_64/cuffdiff --output-dir /data/zhang/makerman/MapSplice/3D.EvC /datafc/zhang/makerman/TopHat/index/h_sapiens_cds.gtf /data/zhang/makerman/MapSplice/BAM/3D.0.sf2.102111.sort.rmdup.bam  /data/zhang/makerman/MapSplice/BAM/3D.0.control.102111.sort.rmdup.bam

#/data/zhang/makerman/MAP_TOOLS/cufflinks-1.1.0.Linux_x86_64/cuffdiff --output-dir /data/zhang/makerman/MapSplice/3D.CvC /datafc/zhang/makerman/TopHat/index/h_sapiens.gtf BAM/3D.1.control.102111.sort.bam  BAM/3D.2.control.102111.sort.bam

/data/zhang/makerman/MAP_TOOLS/cufflinks-1.1.0.Linux_x86_64/cuffdiff --output-dir /data/zhang/makerman/MapSplice/2D.EvC /datafc/zhang/makerman/TopHat/index/h_sapiens_cds.gtf /data/zhang/makerman/MapSplice/BAM/2D.0.sf2.102111.sort.rmdup.bam  /data/zhang/makerman/MapSplice/BAM/2D.0.control.102111.sort.rmdup.bam