141112 HiSeqRapidRun
- WGBS libraries were captured with biotin probes by Noi
Mapping results
Library ID
|
Total sequenced bases
|
Total trimmed bases
|
Total mapped bases
|
%trimmed
|
%mapped
|
SeqCap-pCancerSetA-Nov4_12 |
1,557,796,200 |
1,490,698,729 |
1,183,722,483 |
4.31% |
79.41%
|
SeqCap-pCancerSetA-Nov4_13 |
1,956,384,000 |
1,875,643,861 |
1,441,463,344 |
4.13% |
76.85%
|
SeqCap-pCancerSetA-Nov4_14 |
1,604,724,200 |
1,533,952,230 |
1,236,147,785 |
4.41% |
80.59%
|
SeqCap-pCancerSetA-Nov4_15 |
1,656,779,800 |
1,582,578,941 |
1,278,421,106 |
4.48% |
80.78%
|
SeqCap-pCancerSetA-Nov4_16 |
1,551,344,600 |
1,482,228,220 |
1,172,067,971 |
4.46% |
79.07%
|
SeqCap-pCancerSetA-Nov4_18 |
1,544,614,600 |
1,475,609,077 |
1,188,780,824 |
4.47% |
80.56%
|
SeqCap-pCancerSetA-Nov4_19 |
1,937,986,600 |
1,868,857,625 |
1,466,874,474 |
3.57% |
78.49%
|
SeqCap-pCancerSetA-Nov4_2 |
1,926,683,000 |
1,840,697,493 |
1,484,110,129 |
4.46% |
80.63%
|
SeqCap-pCancerSetA-Nov4_4 |
2,527,810,600 |
2,414,697,940 |
1,897,794,294 |
4.47% |
78.59%
|
SeqCap-pCancerSetA-Nov4_5 |
1,685,759,800 |
1,617,249,202 |
1,293,881,116 |
4.06% |
80.01%
|
SeqCap-pCancerSetA-Nov4_6 |
1,974,733,600 |
1,891,689,068 |
1,507,964,542 |
4.21% |
79.72%
|
SeqCap-pCancerSetA-Nov4_7 |
1,896,482,800 |
1,815,259,906 |
1,391,697,180 |
4.28% |
76.67%
|
SeqCap-pNormalSetA-Nov4_12 |
2,074,019,600 |
1,975,408,680 |
1,571,662,041 |
4.75% |
79.56%
|
SeqCap-pNormalSetA-Nov4_13 |
1,740,938,000 |
1,658,485,066 |
1,318,975,132 |
4.74% |
79.53%
|
SeqCap-pNormalSetA-Nov4_14 |
1,867,843,400 |
1,781,077,564 |
1,442,362,287 |
4.65% |
80.98%
|
SeqCap-pNormalSetA-Nov4_15 |
2,428,342,400 |
2,310,196,699 |
1,966,339,089 |
4.87% |
85.12%
|
SeqCap-pNormalSetA-Nov4_16 |
1,922,011,000 |
1,827,491,168 |
1,448,437,222 |
4.92% |
79.26%
|
SeqCap-pNormalSetA-Nov4_18 |
1,750,909,200 |
1,663,264,442 |
1,302,849,113 |
5.01% |
78.33%
|
SeqCap-pNormalSetA-Nov4_19 |
1,714,868,600 |
1,634,401,979 |
1,295,380,595 |
4.69% |
79.26%
|
SeqCap-pNormalSetA-Nov4_2 |
1,723,048,400 |
1,647,260,004 |
1,359,456,644 |
4.40% |
82.53%
|
SeqCap-pNormalSetA-Nov4_4 |
2,111,874,400 |
2,013,677,234 |
1,563,440,813 |
4.65% |
77.64%
|
SeqCap-pNormalSetA-Nov4_5 |
1,505,598,000 |
1,436,744,421 |
1,126,814,306 |
4.57% |
78.43%
|
SeqCap-pNormalSetA-Nov4_6 |
1,731,991,400 |
1,653,646,386 |
1,314,038,490 |
4.52% |
79.46%
|
SeqCap-pNormalSetA-Nov4_7 |
1,953,762,600 |
1,863,167,423 |
1,495,812,111 |
4.64% |
80.28%
|
Scripts
reads_dir="/oasis/tscc/scratch/ddiep/Working/141117_RRBS/Reads"
cur_dir=`pwd`
cope="/home/ddiep/softwares/cope-src-v1.1.3/src/cope -o connect.fq -2 left1.fq -3 left2.fq -m 0"
#THIS ONE for PE
trim="/home/ddiep/softwares/trim_galore_latest/trim_galore --phred33 --paired --dont_gzip -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT"
#cd $reads_dir
#FILES=`ls *R1_001.fastq`
cd $cur_dir
for f in Sample_NP-SeqCap-pCancerSetA-Nov4_2 Sample_NP-SeqCap-pNormalSetA-Nov4_12 Sample_NP-SeqCap-pNormalSetA-Nov4_13
do
n=`echo $f | sed 's/Sample_NP-//g'`
echo "#!/bin/csh" > $n.job
echo "#PBS -l nodes=1:ppn=2" >> $n.job
echo "#PBS -l walltime=3:00:00" >> $n.job
echo "#PBS -o $n.log" >> $n.job
echo "#PBS -e $n.err" >> $n.job
echo "#PBS -V" >> $n.job
echo "#PBS -M diep.hue.dinh@gmail.com" >> $n.job
echo "#PBS -m abe" >> $n.job
echo "#PBS -A k4zhang-group" >> $n.job
echo "cd /state/partition1/\$USER/\$PBS_JOBID" >> $n.job
echo "zcat $reads_dir/$f/*_R1_*gz > $n.R1.fastq" >> $n.job
echo "zcat $reads_dir/$f/*_R2_*gz > $n.R2.fastq" >> $n.job
echo "$trim $n.R1.fastq $n.R2.fastq" >> $n.job
echo "cp *fq $cur_dir/" >> $n.job
echo "cp *txt $cur_dir/" >> $n.job
qsub -q hotel $n.job
done
#===Change the following paths===#
cur_dir=`pwd`
scripts_dir="/oasis/tscc/scratch/ddiep/BisReadMapper/src"
reads_dir="$cur_dir/Trimmed_reads"
# reference files
ref_dir="/oasis/tscc/scratch/ddiep"
ref_fai="$ref_dir/bisHg19_plusLambda/hg19_lambda.fa.fai"
template_fwd="$ref_dir/bisHg19_plusLambda/hg19_lambda.bis.CT"
template_rev="$ref_dir/bisHg19_plusLambda/hg19_lambda.bis.GA"
# softwares
bwa="/home/ddiep/softwares/bwa-0.7.5a/bwa"
#=== List FASTQ to process ===#
cd $reads_dir
FILES=`ls *val_1.fq`
#FILES="s_1_1_ILMN_Indx01.cope.trimmed.fq"
cd $cur_dir
#===Begin===#
for f in ${FILES}
do
n=`echo $f | sed 's/.R1_val_1.fq//g'`
mkdir $cur_dir/$n
cd $cur_dir/$n
#1) Run mapper:
echo "#!/bin/csh" > $n.job
echo "#PBS -l nodes=1:ppn=4" >> $n.job
echo "#PBS -l walltime=14:00:00" >> $n.job
echo "#PBS -o $n.log" >> $n.job
echo "#PBS -e $n.err" >> $n.job
echo "#PBS -V" >> $n.job
echo "#PBS -M diep.hue.dinh@gmail.com" >> $n.job
echo "#PBS -m abe" >> $n.job
echo "#PBS -A k4zhang-group" >> $n.job
echo "cd /state/partition1/\$USER/\$PBS_JOBID" >> $n.job
echo "cat $reads_dir/${n}.R1_val_1.fq $reads_dir/${n}.R2_val_2.fq > reads.fq" >> $n.job
echo "$scripts_dir/BisReadMapper.pl -r reads.fq -W $template_fwd -C $template_rev -g $ref_fai -a $bwa -b 64 -p 4 -n $n > $n.status" >> $n.job
echo "cp *sam $cur_dir/$n" >> $n.job
echo "cp *status $cur_dir/$n" >> $n.job
echo "ls *sorted.sam > $cur_dir/list_sams" >> $n.job
echo "$scripts_dir/BamExtractor.pl -i $cur_dir/list_sams -s $cur_dir/list_paths_Hg19 -o $n -r none -v no -b no -p no -d 5" >> $n.job
echo "cp *bam $cur_dir/$n" >> $n.job
echo "cp *methylFreq $cur_dir/$n" >> $n.job
qsub -q hotel $n.job
done
#===End===#
Assessment of capturing performance
Sample
|
total_bases_coverred
|
total_bases
|
on_target_bases_covered
|
on_target_bases
|
Specificity
|
target_coverred
|
Enrichment_factor
|
SeqCap-pCancerSetA-Nov4_12 |
138,931,528 |
1,168,877,279 |
5,883,919 |
450,558,243 |
38.5% |
20.0% |
63
|
SeqCap-pCancerSetA-Nov4_13 |
369,134,874 |
1,424,314,151 |
21,209,194 |
614,835,055 |
43.2% |
72.2% |
77
|
SeqCap-pCancerSetA-Nov4_14 |
302,700,391 |
1,203,488,680 |
13,952,014 |
489,036,528 |
40.6% |
47.5% |
69
|
SeqCap-pCancerSetA-Nov4_15 |
277,562,818 |
1,250,329,814 |
12,577,032 |
511,943,961 |
40.9% |
42.8% |
70
|
SeqCap-pCancerSetA-Nov4_16 |
274,256,170 |
1,164,394,023 |
12,418,863 |
474,550,198 |
40.8% |
42.3% |
70
|
SeqCap-pCancerSetA-Nov4_18 |
403,128,602 |
1,170,296,929 |
23,073,184 |
461,126,140 |
39.4% |
78.5% |
66
|
SeqCap-pCancerSetA-Nov4_19 |
385,167,143 |
1,417,434,873 |
22,614,122 |
614,480,251 |
43.4% |
77.0% |
77
|
SeqCap-pCancerSetA-Nov4_2 |
354,784,810 |
1,514,708,612 |
19,490,111 |
751,025,646 |
49.6% |
66.3% |
99
|
SeqCap-pCancerSetA-Nov4_4 |
352,108,468 |
2,000,885,721 |
23,609,719 |
1,141,652,594 |
57.1% |
80.3% |
134
|
SeqCap-pCancerSetA-Nov4_5 |
196,108,966 |
1,300,234,129 |
8,246,274 |
563,004,318 |
43.3% |
28.1% |
77
|
SeqCap-pCancerSetA-Nov4_6 |
450,502,450 |
1,502,032,451 |
28,135,196 |
645,300,745 |
43.0% |
95.7% |
76
|
SeqCap-pCancerSetA-Nov4_7 |
226,755,475 |
1,432,933,860 |
10,016,683 |
629,536,922 |
43.9% |
34.1% |
79
|
SeqCap-pNormalSetA-Nov4_12 |
368,272,742 |
1,450,833,379 |
32,791,421 |
853,947,465 |
58.9% |
111.6% |
145
|
SeqCap-pNormalSetA-Nov4_13 |
330,611,335 |
1,291,478,405 |
29,764,564 |
756,289,960 |
58.6% |
101.3% |
143
|
SeqCap-pNormalSetA-Nov4_14 |
360,000,998 |
1,364,998,815 |
32,082,346 |
801,469,734 |
58.7% |
109.2% |
144
|
SeqCap-pNormalSetA-Nov4_15 |
375,193,438 |
1,970,841,697 |
30,241,737 |
1,295,408,500 |
65.7% |
102.9% |
194
|
SeqCap-pNormalSetA-Nov4_16 |
365,138,307 |
1,417,821,628 |
31,787,247 |
825,520,233 |
58.2% |
108.2% |
141
|
SeqCap-pNormalSetA-Nov4_18 |
326,952,891 |
1,305,603,890 |
28,937,598 |
760,701,025 |
58.3% |
98.5% |
141
|
SeqCap-pNormalSetA-Nov4_19 |
312,924,926 |
1,271,134,775 |
27,505,559 |
749,645,411 |
59.0% |
93.6% |
145
|
SeqCap-pNormalSetA-Nov4_2 |
353,552,883 |
1,275,196,941 |
31,331,422 |
731,603,678 |
57.4% |
106.6% |
136
|
SeqCap-pNormalSetA-Nov4_4 |
354,621,865 |
1,456,339,179 |
31,829,571 |
867,560,025 |
59.6% |
108.3% |
149
|
SeqCap-pNormalSetA-Nov4_5 |
291,891,632 |
1,066,253,299 |
27,061,797 |
618,610,388 |
58.0% |
92.1% |
140
|
SeqCap-pNormalSetA-Nov4_6 |
333,830,242 |
1,234,362,498 |
31,357,436 |
723,278,371 |
58.6% |
106.7% |
143
|
SeqCap-pNormalSetA-Nov4_7 |
377,475,888 |
1,451,628,039 |
32,325,421 |
843,343,133 |
58.1% |
110.0% |
140
|
|