Dinh/Dinh 2013/NOTES/2013-1-7: Difference between revisions

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>Dinh
(Created page with "==bisReadMapper pipeline== ===Triton=== * Write a shell script as follows: <nowiki> # current directory: change the following path to your working directory. cur_dir="/oasis...")
 
>Dinh
mNo edit summary
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===Triton===
===Triton===
* Write a shell script as follows:
* First map reads using a shell script:
* Edit '''Go.mapBisulfite.sh''' as follows:
  <nowiki>
  <nowiki>
### EDIT below ####
# current directory: change the following path to your working directory.
# current directory: change the following path to your working directory.
cur_dir="/oasis/triton/scratch/ddiep/Working/WGBS_Noi_hg19/HELLO"
cur_dir="/oasis/triton/scratch/ddiep/Working/WGBS_Noi_hg19/HELLO"
Line 11: Line 14:
reads_dir="/oasis/triton/scratch/ddiep/Working/WGBS_Noi_hg19/HELLO"
reads_dir="/oasis/triton/scratch/ddiep/Working/WGBS_Noi_hg19/HELLO"


# List the index names (or unique names to each read files
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
### DO NOT EDIT, unless you know where these files are ####
# the following paths should stay the same on triton.  
# the following paths should stay the same on triton.  
bisReadMapper="/home/ddiep/scripts/MethylationPipeline/smartBisReadMapper.pl"
bisReadMapper="/home/ddiep/scripts/MethylationPipeline/smartBisReadMapper.pl"
template_fwd="/projects/zhang-lab/ddiep/LatestGenome/bisHg19/hg19.fa.bis.fwd.index"
template_fwd="/projects/zhang-lab/ddiep/LatestGenome/BisRef/bisHg19/hg19.fa.bis.fwd.index"
template_rev="/projects/zhang-lab/ddiep/LatestGenome/bisHg19/hg19.fa.bis.rev.index"
template_rev="/projects/zhang-lab/ddiep/LatestGenome/BisRef/bisHg19/hg19.fa.bis.rev.index"
template_fa="/projects/zhang-lab/ddiep/LatestGenome/bisHg19/hg19.fa"
template_fa="/projects/zhang-lab/ddiep/LatestGenome/BisRef/bisHg19/hg19.fa"
soap="/home/ddiep/softwares/soap2.21release/soap"
soap="/home/ddiep/softwares/soap2.21release/soap"
############################################################


cd $cur_dir
cd $cur_dir
INDX="Indx1 Indx2 Indx3"


for n in ${INDX}
for n in ${INDX}
do
do
  f="s_1_1_$n.txt"
  f="s_1_1_$n.txt" # name format for read 1, make sure it matches the file names
  g="s_1_2_$n.txt"
  g="s_1_2_$n.txt" # name format for read 2, make sure it matches the file names
  echo "#!/bin/csh" > $n.job
  echo "#!/bin/csh" > $n.job
  echo "#PBS -q small" >> $n.job
  echo "#PBS -q small" >> $n.job
Line 38: Line 53:
  echo "cd $cur_dir" >> $n.job
  echo "cd $cur_dir" >> $n.job


  echo "$bisReadMapper -r $reads_dir/$f,$reads_dir/$g -m 2 -W $template_fwd -C $template_rev -g $template_fa -a $soap -b 33 -p 8 -n $n -q 20  > $n.status" >> $n.job
  echo "$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
  echo "rm *encoded" >> $n.job
  qsub $n.job
  qsub $n.job


done
done</nowiki>
 
* Run the script:
</nowiki>
sh Go.mapBisulfite.sh

Revision as of 02:45, 11 January 2013

bisReadMapper pipeline

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 files
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


### 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=8" >> $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 diep.hue.dinh@gmail.com" >> $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