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

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  ./bisMapSoapTriton.pl [FILENAME] 80
  ./bisMapSoapTriton.pl [FILENAME] 80
* Mapping sequences 20bp trimmed from 5'end and 6bp trimmed from 3'end
* Mapping sequences 20bp trimmed from 5'end and 6bp trimmed from 3'end
  the last two lines of SEmapping.template
  The last two lines of SEmapping.template
  cd /home/nplongthongkum/Labdir/BSPP/Noi_Data/LC_120426_HL118.hg18_trim5-20/mapping_trimm5-20_3-6
  cd /home/nplongthongkum/Labdir/BSPP/Noi_Data/LC_120426_HL118.hg18_trim5-20/mapping_trimm5-20_3-6
  ../bisMapSoapTriton.pl [FILENAME] 75
  ../bisMapSoapTriton.pl [FILENAME] 75

Revision as of 04:20, 14 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 to map the sequences to hg18 and do the same thing as I did before with the previous data set to be able to compare the quality of sequencing and protocol. I repeated mapping again on Triton cluster

Mapping to hg18 (on Triton cluster)

  • Note: * I also trimmed 6 bp from 3' end as previously did even the quality of sequencing was good.
  • Mapping sequences 20bp trimmed from 5'end
The last two lines of SEmapping.template 
cd /home/nplongthongkum/Labdir/BSPP/Noi_Data/LC_120426_HL118.hg18_trim5-20
./bisMapSoapTriton.pl [FILENAME] 80
  • Mapping sequences 20bp trimmed from 5'end and 6bp trimmed from 3'end
The last two lines of SEmapping.template
cd /home/nplongthongkum/Labdir/BSPP/Noi_Data/LC_120426_HL118.hg18_trim5-20/mapping_trimm5-20_3-6
../bisMapSoapTriton.pl [FILENAME] 75
  • Then calculate specificity and on-target coverage 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

Summary of mapping data

Trimmed 20bp from 5' end

Sample IDs # of reads Total sequences (bps) # of CpGs called Read mapping rate (%)
PGP1-F 54C 22,049,038 2,204,903,800 131,416 41.86
PGP1-iPS 54C 20,159,226 2,015,922,600 105,280 48.89
H1 54C 28,060,038 2,806,003,800 162,709 41.75


Specificity and target coverage

PGP1F-54C		
###########################		
Total mapppable bases	676,624,800	
Total on-target bases	590,092,713	
Specificity	0.8721	
###########################		
total capture targets	262,586	bp
DP>=1x	261,167	0.994596056
DP>=10x	260,240	0.991065784
DP>=20x	98,519	0.375187558		
PGP1iPS-54C		
###########################		
Total mapppable bases	723,009,280	
Total on-target bases	608,068,758	
Specificity	0.841	
###########################		
total capture targets	210,284	bp
DP>=1x	209,072	0.994236366
DP>=10x	208,454	0.991297483
DP>=20x	100,248	0.476726712				
###########################		
Total mapppable bases	863,980,560	
Total on-target bases	745,163,756	
Specificity	0.8625	
###########################		
total capture targets	324,890	bp
DP>=1x	323,276	0.995032165
DP>=10x	322,108	0.991437102
DP>=20x	110,768	0.34094001

Trimmed 20bp from 5' end and 6bp from 3' end

Sample IDs # of reads Total sequences (bps) # of CpGs called Read mapping rate (%)
PGP1-F 54C 22,049,038 2,204,903,800 135,467 43.79
PGP1-iPS 54C 20,159,226 2,015,922,600 106,535 50.69
H1 54C 28,060,038 2,806,003,800 167,445 43.59


Specificity and target coverage calculation

PGP1F-54C		
###########################		
Total mapppable bases	662,414,250	
Total on-target bases	576,137,096	
Specificity	0.8698	
###########################		
total capture targets	270,682	bp
DP>=1x	269,065	0.9940262
DP>=10x	267,989	0.990051056
DP>=20x	102,254	0.377764314		
PGP1iPS-54C		
###########################		
Total mapppable bases	700,625,100	
Total on-target bases	583,970,343	
Specificity	0.8335	
###########################		
total capture targets	212,810	bp
DP>=1x	211,437	0.993548236
DP>=10x	210,768	0.990404586
DP>=20x	102,285	0.480640008		
H1-54C		
###########################		
Total mapppable bases	843,865,950	
Total on-target bases	724,892,066	
Specificity	=	0.859
###########################		
total capture targets	334,358	bp
DP>=1x	332,505	0.994458036
DP>=10x	331,175	0.990480264
DP>=20x	114,674	0.342967717
  • Note: actually there is no need to map RC-1 sample since this library was not capture with bisulfite padlock probe.