Noi/NOTES/2012-6-27: Difference between revisions
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less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx80.txt | /home/kunzhang/bin/trimFastq.pl 27 83> GM12878-H0 | less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx80.txt | /home/kunzhang/bin/trimFastq.pl 27 83> GM12878-H0 | ||
== Mapping to hg19 (on Triton cluster) == | == 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/120608_SN1001_ASM-ASCM_20120627 | |||
./bisReadMapperSE19Triton.pl [FILENAME] 83 | |||
* 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 | |||
== Summary of mapping data == | |||
{| {{table}} border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Sample IDs''' | |||
| align="center" style="background:#f0f0f0;"|'''# of reads''' | |||
| align="center" style="background:#f0f0f0;"|'''Total sequences (bps)''' | |||
| align="center" style="background:#f0f0f0;"|'''# of CpGs called''' | |||
| align="center" style="background:#f0f0f0;"|'''Read mapping rate (%)''' | |||
|- | |||
| DF2||8,943,862||983,824,820||392,505||76.96 | |||
|- | |||
| GM12878-H0||9,336,524||1,027,017,640||390,506||79.38 | |||
|- | |||
| GM12878||7,395,278||813,480,580||333,453||81.85 | |||
|- | |||
| H0||9,208,510||1,012,936,100||398,481||77.31 | |||
|- | |||
| H14||8,087,240||889,596,400||341,384||82.64 | |||
|- | |||
| H16||9,443,812||1,038,819,320||400,255||78.32 | |||
|- | |||
| H7||6,294,626||692,408,860||292,285||80.06 | |||
|- | |||
| P10E3||6,633,346||729,668,060||312,365||79.02 | |||
|} |
Revision as of 23:03, 27 June 2012
Mapping of ASM and ASCM samples in human cells project to hg19
- Refer to the capture experiment on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-24, http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-31
- The libraries were sequenced on HiSeq 120608_SN1001 run (at Biogem) ,lane 8.
- Sequencing data on genome-miner: /media/SeqStore2/120608_SN1001/BSPP
Sample indexes
Sample IDs | Index |
GM12878 | AmpR6.3.Ind73 |
P10E3 | AmpR6.3.Ind74 |
DF2 | AmpR6.3.Ind75 |
H0 | AmpR6.3.Ind76 |
H7 | AmpR6.3.Ind77 |
H14 | AmpR6.3.Ind78 |
H16 | AmpR6.3.Ind79 |
GM12878:H0 1:1 | AmpR6.3.Ind80 |
Concatenate sequences and trim 27 bp from 5'end (on genome-miner)
* Note: Length of the raw data 110bp less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx73.txt | /home/kunzhang/bin/trimFastq.pl 27 83> GM12878 less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx74.txt | /home/kunzhang/bin/trimFastq.pl 27 83> P10E3 less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx75.txt | /home/kunzhang/bin/trimFastq.pl 27 83> DF2 less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx76.txt | /home/kunzhang/bin/trimFastq.pl 27 83> H0 less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx77.txt | /home/kunzhang/bin/trimFastq.pl 27 83> H7 less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx78.txt | /home/kunzhang/bin/trimFastq.pl 27 83> H14 less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx79.txt | /home/kunzhang/bin/trimFastq.pl 27 83> H16 less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx80.txt | /home/kunzhang/bin/trimFastq.pl 27 83> GM12878-H0
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/120608_SN1001_ASM-ASCM_20120627 ./bisReadMapperSE19Triton.pl [FILENAME] 83
- 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
Summary of mapping data
Sample IDs | # of reads | Total sequences (bps) | # of CpGs called | Read mapping rate (%) |
DF2 | 8,943,862 | 983,824,820 | 392,505 | 76.96 |
GM12878-H0 | 9,336,524 | 1,027,017,640 | 390,506 | 79.38 |
GM12878 | 7,395,278 | 813,480,580 | 333,453 | 81.85 |
H0 | 9,208,510 | 1,012,936,100 | 398,481 | 77.31 |
H14 | 8,087,240 | 889,596,400 | 341,384 | 82.64 |
H16 | 9,443,812 | 1,038,819,320 | 400,255 | 78.32 |
H7 | 6,294,626 | 692,408,860 | 292,285 | 80.06 |
P10E3 | 6,633,346 | 729,668,060 | 312,365 | 79.02 |