Noi/NOTES/2012-5-7: Difference between revisions

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  /home/kunzhang/bin/bisPileupPair2coverage.pl PGP1iPS-54C.fwd.pileup.methylFreq.BED.txt PGP1iPS-54C.fwd.pileup PGP1iPS-54C.rev.pileup > target_PGP1iPS-54C
  /home/kunzhang/bin/bisPileupPair2coverage.pl PGP1iPS-54C.fwd.pileup.methylFreq.BED.txt PGP1iPS-54C.fwd.pileup PGP1iPS-54C.rev.pileup > target_PGP1iPS-54C
  /home/kunzhang/bin/bisPileupPair2coverage.pl H1-54C.fwd.pileup.methylFreq.BED.txt H1-54C.fwd.pileup H1-54C.rev.pileup > target_H1-54C
  /home/kunzhang/bin/bisPileupPair2coverage.pl H1-54C.fwd.pileup.methylFreq.BED.txt H1-54C.fwd.pileup H1-54C.rev.pileup > target_H1-54C
* I also tried to trim 6 bp from 3' end as previously did even the quality of sequencing was good.

Revision as of 22:34, 10 May 2012

Mapping of PGP1-F PGP1-iPS and H1 samples captured with LC Sciences probe set

Sample index

Sample IDs Index
PGP1-F 54C CA-2-FA.Ind7.Sol
PGP1-iPS 54C CA-2-FA.Ind45.Sol
H1 54C CA-2-FA.Ind76.Sol
RC-1 CA-2-FA.Indx77.Sol
  • Note: RC-1 is the library from Baylor
  • Refer to the previous batch (111012_HL105), the sequences were trimmed 20bp from 5' end and also 6bp from 3' end since the quality of that run was not good as usual. However the quality of this run seemed to be good. I will trim only 20bp from the 5'end.

Trimming 20 bp from 5'end (on genome-miner)

less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx7.txt | /home/kunzhang/bin/trimFastq.pl	20 80 > ./PGP1F-54C
less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx45.txt | /home/kunzhang/bin/trimFastq.pl  20 80 > ./PGP1iPS-54C
less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx76.txt | /home/kunzhang/bin/trimFastq.pl  20 80 > ./H1-54C
less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx77.txt | /home/kunzhang/bin/trimFastq.pl  20 80 > ./RC-1

Mapping to hg19 (on Triton cluster)

Generate job files and submit jobs

  • SEmapping.template
#!/bin/csh
#PBS -q small 
#PBS -l nodes=1:ppn=2
#PBS -l walltime=12:00:00
#PBS -o [FILENAME]_SEmapping.log 
#PBS -e [FILENAME]_SEmapping.err
#PBS -V
#PBS -M nongluk6665@gmail.com 
#PBS -m abe
#PBS -A zhang-lab
cd /home/nplongthongkum/Labdir/BSPP/Noi_Data/LC_120426_HL118.hg19
./bisReadMapperSE19Triton_b.pl [FILENAME] 80
  • generate_jobs.sh
#!/bin/bash
scriptname="qsub_script.sh"
echo "#!/bin/bash" > $scriptname
chmod +x $scriptname
for f in * 
 do
 if [ `expr index $f "."` -eq 0 ]
     then
     sed "s/\[FILENAME\]/$f/g" SEmapping.template > SEmapping_$f.job
     echo "qsub SEmapping_$f.job" >> $scriptname
 fi
done
  • qsub_script.sh
qsub SEmapping_H1-54C.job
qsub SEmapping_PGP1F-54C.job
qsub SEmapping_PGP1iPS-54C.job
qsub SEmapping_RC-1.job
  • I'm supposed map the sequences to hg18. I repeated mapping again on Triton cluster
BED count 
 162,709 H1-54C.fwd.pileup.methylFreq.BED.txt
 131,416 PGP1F-54C.fwd.pileup.methylFreq.BED.txt
 105,280 PGP1iPS-54C.fwd.pileup.methylFreq.BED.txt
  • Then calculate specificity and on-target using Dr. Zhang script
/home/kunzhang/bin/bisPileupPair2coverage.pl PGP1F-54C.fwd.pileup.methylFreq.BED.txt  PGP1F-54C.fwd.pileup PGP1F-54C.rev.pileup > target_PGP1F-54C
/home/kunzhang/bin/bisPileupPair2coverage.pl PGP1iPS-54C.fwd.pileup.methylFreq.BED.txt PGP1iPS-54C.fwd.pileup PGP1iPS-54C.rev.pileup > target_PGP1iPS-54C
/home/kunzhang/bin/bisPileupPair2coverage.pl H1-54C.fwd.pileup.methylFreq.BED.txt H1-54C.fwd.pileup H1-54C.rev.pileup > target_H1-54C
  • I also tried to trim 6 bp from 3' end as previously did even the quality of sequencing was good.