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===Triton=== * First map reads using a shell script: * Edit '''Go.mapBisulfite.sh''' as follows: ### EDIT below #### # current directory: change the following path to your working directory. '''cur_dir="/oasis/triton/scratch/ddiep/Working/WGBS_Noi_hg19/HELLO"''' # reads directory: change the following path to the reads directory # reads_dir and cur_dir doesn't have to be the same '''reads_dir="/oasis/triton/scratch/ddiep/Working/WGBS_Noi_hg19/HELLO"''' # List the index names (or unique names to each read) '''INDX="Indx1 Indx2 Indx3"''' '''email="ddiep@ucsd.edu"''' '''mm=2''' # max number of allowable mismatches '''qual=64''' # base quality offset value '''qtrim=20''' # Phred quality value for soft-trimming '''threetrim=0''' # number of bases to trim from 3' end (rightmost) '''fivetrim=0''' # number of bases to trim from 5' end (leftmost) '''p=8''' # number of parallel threads to use. ### DO NOT EDIT, unless you know where these files are #### # the following paths should stay the same on triton. bisReadMapper="/home/ddiep/scripts/MethylationPipeline/smartBisReadMapper.pl" template_fwd="/projects/zhang-lab/ddiep/LatestGenome/BisRef/bisHg19/hg19.fa.bis.fwd.index" template_rev="/projects/zhang-lab/ddiep/LatestGenome/BisRef/bisHg19/hg19.fa.bis.rev.index" template_fa="/projects/zhang-lab/ddiep/LatestGenome/BisRef/bisHg19/hg19.fa" soap="/home/ddiep/softwares/soap2.21release/soap" ############################################################ cd $cur_dir for n in ${INDX} do ### '''f="s_1_1_$n.txt" # name format for read 1, make sure it matches the file names''' '''g="s_1_2_$n.txt" # name format for read 2, make sure it matches the file names''' ### echo "#!/bin/csh" > $n.job echo "#PBS -q small" >> $n.job echo "#PBS -l nodes=1:ppn=$p" >> $n.job echo "#PBS -l walltime=36:00:00" >> $n.job echo "#PBS -o $n.log" >> $n.job echo "#PBS -e $n.err" >> $n.job echo "#PBS -V" >> Idx$n.job echo "#PBS -M $email" >> $n.job echo "#PBS -m abe" >> $n.job echo "#PBS -A zhang-lab" >> $n.job echo "cd $cur_dir" >> $n.job echo "$bisReadMapper -r $reads_dir/$f,$reads_dir/$g -m $mm -W $template_fwd -C $template_rev -g $template_fa -a $soap -b $qual -p $p -n $n -q $qtrim -5 $fivetrim -3 $threetrim > $n.status" >> $n.job echo "rm *encoded" >> $n.job qsub $n.job done * Run the script: sh Go.mapBisulfite.sh > job_ids * Now, there will be a different job for each sequence file that you have. * If you have multiple sequencing lanes, just change the '''f''' and '''g''' variables to s_2, s_3, etc, and re-run the shell script with the command above. * Check the mapping progress by looking at the Indx#.status file * OR check the job by: qstat -u ddiep * To delete the job: qdel job#
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