Noi/NOTES/2012-6-27

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Mapping of ASM and ASCM samples in human cells project to hg19[edit]

Sample indexes[edit]

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)[edit]

* 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)[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/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[edit]

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
  • Mapping data directory on genome-miner: /home/nplongth/Noi_scratch/120608_SN1001_ASM-ASCM_20120627/hg19.mapping