Dinh/Dinh 2014/NOTES/2014-11-17
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141112 HiSeqRapidRun[edit]
- WGBS libraries were captured with biotin probes by Noi: Noi/NOTES/2014-11-4
Mapping results[edit]
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[edit]
- Go.trimReads.sh
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 $n.job done
- Go.Map.sh
#===Change the following paths===# cur_dir=`pwd` scripts_dir="/oasis/tscc/scratch/ddiep/BisReadMapper/src" reads_dir="$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[edit]
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 |
Assessing the complexity of each library[edit]
- Count the number of starting positions in each BAM file in non-overlapping 50 bp bins
- Normalize each bin count by per million mapped reads
- Plot the density for each file. Y-axis is the frequency of each count, X-axis is the log2(normalized counts).
- Normal samples have greater complexity because most bins have fewer counts whereas cancer have more bins with higher counts (more reads covering same bins).
- Cancer samples
File:141112 HiSeqRapidRun cancer samples 50bp coverage.png
- Normal samples