Revision as of 23:17, 27 June 2012 by >Noi
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
#!/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