Noi/NOTES/2012-5-7: Difference between revisions
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* The libraries were sequenced on 120426_HL118 run,lane 5. | * The libraries were sequenced on 120426_HL118 run,lane 5. | ||
* Sequencing data on genome-miner: /home/kunzhang/seqStore/120426_HL118/PE | * Sequencing data on genome-miner: /home/kunzhang/seqStore/120426_HL118/PE | ||
== Sample | == Sample indexes == | ||
{| {{table}} | {| {{table}} | ||
| align="center" style="background:#f0f0f0;"|'''Sample IDs''' | | align="center" style="background:#f0f0f0;"|'''Sample IDs''' | ||
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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_*_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 | less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx77.txt | /home/kunzhang/bin/trimFastq.pl 20 80 > ./RC-1 | ||
on different directory | |||
less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx7.txt.gz | /home/kunzhang/bin/trimFastq.pl 20 75 > ./PGP1F-54C | |||
less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx45.txt.gz | /home/kunzhang/bin/trimFastq.pl 20 75 > ./PGP1iPS-54C | |||
less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx76.txt.gz | /home/kunzhang/bin/trimFastq.pl 20 75 > ./H1-54C | |||
== Mapping to hg19 (on Triton cluster) == | == Mapping to hg19 (on Triton cluster) == | ||
'''Generate job files and submit jobs'''<br> | '''Generate job files and submit jobs'''<br> | ||
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qsub SEmapping_PGP1iPS-54C.job | qsub SEmapping_PGP1iPS-54C.job | ||
qsub SEmapping_RC-1.job | qsub SEmapping_RC-1.job | ||
* I'm supposed map the sequences to hg18. I repeated mapping again on Triton cluster | * 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) == | == 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. | * 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 | *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 | cd /home/nplongthongkum/Labdir/BSPP/Noi_Data/LC_120426_HL118.hg18_trim5-20 | ||
./bisMapSoapTriton.pl [FILENAME] 80 | ./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 | 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 | ||
* Then calculate specificity and on-target coverage using Dr. Zhang script | * Then calculate specificity and on-target coverage using Dr. Zhang script (on genome-miner) | ||
'''Directories:''' | |||
/home/nplongth/Noi_scratch/LC_120426_HL118/hg18.mapping_trim_20-75 | |||
/home/nplongth/Noi_scratch/LC_120426_HL118/hg18.mapping_trim_20-80 | |||
/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 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 PGP1iPS-54C.fwd.pileup.methylFreq.BED.txt PGP1iPS-54C.fwd.pileup PGP1iPS-54C.rev.pileup > target_PGP1iPS-54C | ||
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|}<br> | |}<br> | ||
'''Specificity and target coverage'''<br> | '''Specificity and target coverage'''<br> | ||
PGP1F-54C | '''PGP1F-54C''' | ||
########################### | ########################### | ||
Total mapppable bases 676,624,800 | Total mapppable bases 676,624,800 | ||
Line 99: | Line 109: | ||
DP>=1x 261,167 0.994596056 | DP>=1x 261,167 0.994596056 | ||
DP>=10x 260,240 0.991065784 | DP>=10x 260,240 0.991065784 | ||
DP>=20x 98,519 0.375187558 | DP>=20x 98,519 0.375187558 | ||
PGP1iPS-54C | |||
'''PGP1iPS-54C''' | |||
########################### | ########################### | ||
Total mapppable bases 723,009,280 | Total mapppable bases 723,009,280 | ||
Line 109: | Line 120: | ||
DP>=1x 209,072 0.994236366 | DP>=1x 209,072 0.994236366 | ||
DP>=10x 208,454 0.991297483 | DP>=10x 208,454 0.991297483 | ||
DP>=20x 100,248 0.476726712 | DP>=20x 100,248 0.476726712 | ||
'''H1-54C''' | |||
########################### | ########################### | ||
Total mapppable bases 863,980,560 | Total mapppable bases 863,980,560 | ||
Line 134: | Line 147: | ||
|}<br> | |}<br> | ||
'''Specificity and target coverage calculation'''<br> | '''Specificity and target coverage calculation'''<br> | ||
PGP1F-54C | '''PGP1F-54C''' | ||
########################### | ########################### | ||
Total mapppable bases 662,414,250 | Total mapppable bases 662,414,250 | ||
Line 143: | Line 156: | ||
DP>=1x 269,065 0.9940262 | DP>=1x 269,065 0.9940262 | ||
DP>=10x 267,989 0.990051056 | DP>=10x 267,989 0.990051056 | ||
DP>=20x 102,254 0.377764314 | DP>=20x 102,254 0.377764314 | ||
PGP1iPS-54C | |||
'''PGP1iPS-54C''' | |||
########################### | ########################### | ||
Total mapppable bases 700,625,100 | Total mapppable bases 700,625,100 | ||
Line 153: | Line 167: | ||
DP>=1x 211,437 0.993548236 | DP>=1x 211,437 0.993548236 | ||
DP>=10x 210,768 0.990404586 | DP>=10x 210,768 0.990404586 | ||
DP>=20x 102,285 0.480640008 | DP>=20x 102,285 0.480640008 | ||
H1-54C | |||
'''H1-54C''' | |||
########################### | ########################### | ||
Total mapppable bases 843,865,950 | Total mapppable bases 843,865,950 | ||
Total on-target bases 724,892,066 | Total on-target bases 724,892,066 | ||
Specificity | Specificity 0.859 | ||
########################### | ########################### | ||
total capture targets 334,358 bp | total capture targets 334,358 bp |
Latest revision as of 18:06, 27 June 2012
Mapping of PGP1-F PGP1-iPS and H1 samples captured with LC Sciences probe set[edit]
- 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 indexes[edit]
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)[edit]
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 on different directory less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx7.txt.gz | /home/kunzhang/bin/trimFastq.pl 20 75 > ./PGP1F-54C less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx45.txt.gz | /home/kunzhang/bin/trimFastq.pl 20 75 > ./PGP1iPS-54C less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx76.txt.gz | /home/kunzhang/bin/trimFastq.pl 20 75 > ./H1-54C
Mapping to hg19 (on Triton cluster)[edit]
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)[edit]
- 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 (on genome-miner)
Directories: /home/nplongth/Noi_scratch/LC_120426_HL118/hg18.mapping_trim_20-75 /home/nplongth/Noi_scratch/LC_120426_HL118/hg18.mapping_trim_20-80 /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[edit]
Trimmed 20bp from 5' end[edit]
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
H1-54C ########################### 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[edit]
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.