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
- Refer to the capture experiment on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-23
- The libraries were sequenced on 120426_HL118 run,lane 5.
- Sequencing data on genome-miner: /home/kunzhang/seqStore/120426_HL118/PE
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.