Ns126:DennisLo2015-PNAS: Difference between revisions
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>Shicheng |
>Shicheng |
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(14 intermediate revisions by the same user not shown) | |||
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===Data Introduction=== | ===Data Introduction=== | ||
* [[File Name Index and Sample ID]] | |||
* [[94 Samples included (61 single-end, 33 paired-end)]]: | * [[94 Samples included (61 single-end, 33 paired-end)]]: | ||
1) Normal pregnancies ('''17''' sample, paired-end) | 1) Normal pregnancies ('''17''' sample, paired-end) | ||
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cd /home/shg047/oasis/DennisLo2015/fastq_trim | cd /home/shg047/oasis/DennisLo2015/fastq_trim | ||
ls *fq.gz # 127 trimed fastq file | ls *fq.gz # 127 trimed fastq file | ||
gzip -frtv9 * | |||
* md5sum | * md5sum | ||
md5sum *gz > md5sum.bak | md5sum *gz > md5sum.bak | ||
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=== Bam to Hapinfo === | === Bam to Hapinfo === | ||
*Bam merge (forget it, so I just use the run1): | |||
Pregnancy.8.run1.read1.hapInfo.txt Pregnancy.8.run2.read1.hapInfo.txt | |||
Pregnancy.9.run1.read1.hapInfo.txt Pregnancy.9.run2.read1.hapInfo.txt | |||
*Deduplicate to Bam files | |||
deduplicate_bismark -s --bam CTR114_trimmed.fq.gz_bismark_bt2.bam # CTR114_trimmed.fq.gz_bismark_bt2.deduplicated.bam will be created | |||
* Bam to hapinfo | |||
cd /oasis/tscc/scratch/ddiep/DennisLo_WGBS_BAMfiles | cd /oasis/tscc/scratch/ddiep/DennisLo_WGBS_BAMfiles | ||
cd /home/shg047/oasis/DennisLo2015/hapinfo | cd /home/shg047/oasis/DennisLo2015/hapinfo | ||
perl ~/bin/[[samInfoPrep4Bam2Hapinfo.pl]] /oasis/tscc/scratch/ddiep/DennisLo_WGBS_BAMfiles/ > saminfo.txt | perl ~/bin/[[samInfoPrep4Bam2Hapinfo.pl]] /oasis/tscc/scratch/ddiep/DennisLo_WGBS_BAMfiles/ > saminfo.txt | ||
perl [[~/bin/bam2hapInfo2PBS.pl]] saminfo.txt | perl [[~/bin/bam2hapInfo2PBS.pl]] saminfo.txt | ||
* Dinh | * Dinh help me to finish the Bam File, At the same time, I also aligned them by myself again to check the difference. | ||
cd /home/shg047/oasis/DennisLo2015/sortbam | cd /home/shg047/oasis/DennisLo2015/sortbam | ||
perl ~/bin/samInfoPrep4Bam2Hapinfo.pl ./ > ../Saminfo4bam2hapinfo.txt | perl ~/bin/samInfoPrep4Bam2Hapinfo.pl ./ > ../Saminfo4bam2hapinfo.txt | ||
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=== Methylation Haplotype Load === | === Methylation Haplotype Load === | ||
* Distribution in Samples | * Distribution in Samples[[ScatterPlot-File:6681.tm.png.R]] | ||
*MHL:[[File:66F0.tm-mhl-dennislo.png|400px]] MF:[[File:6681.tm.png|400px]] | *MHL:[[File:66F0.tm-mhl-dennislo.png|400px]] MF:[[File:6681.tm.png|400px]] MHLvsMF[[File:7254.tm.png|400px]] Hist:[[File:7BC8.tm.png|400px]] | ||
* [[MHL vs Methylation Freqency from PileOMeth]] | |||
*MHL vs MF: [[File:3E18.tm.png|400px]] * PileOMeth-MF vs Hapinfo-MF:[[File:46F2.tm.png|400px]] |
Latest revision as of 22:34, 31 May 2016
Motivation and Discovery[edit]
Data Introduction[edit]
1) Normal pregnancies (17 sample, paired-end) 2) Organ transplantation patients (7 samples, paired-end) 3) Pregnancies with trisomy 21 fetus (5 samples, paired-end) 4) Lymphoma case (4 sample, paired-end, multiple sequencing runs) 5) Healthy control plasma samples (32 samples, single-end) 6) Hepatocellular carcinoma (HCC) patient samples (29 samples, single-end)
Data Storage[edit]
- Data Download
wget -m --ftp-user=plamethy --ftp-password='de$*d@s3' ftp://137.189.133.62/ ftp 137.189.133.62 Username: plamethy Password: de$*d@s3
- fastq file: shg047@genome-miner.ucsd:/media/TmpStore1/DennisLo2015
- Readme: File:DennisLo2015-Readme.txt
- bam file:
1, Bismark version: /home/shg047/oasis/DennisLo2015/bam 2, bisreadmap version: /oasis/tscc/scratch/ddiep/DennisLo_WGBS_BAMfiles 3, rename bam file: perl renameBamFile.pl
Data Re-analysis[edit]
Trim_galore[edit]
- do the trim_galore and bismark one by one to avoid the OUTPUT error
cd /home/shg047/oasis/DennisLo2015/fastq_trim ls *fq.gz # 127 trimed fastq file gzip -frtv9 *
- md5sum
md5sum *gz > md5sum.bak DennisLo's trimed fastq md5sum
Bismark Alignment[edit]
- analysis the data with free glean quene
- mulitple core=6 will use 128G memory.
- the data is complicated since single-end and pair-end samples are mixed
cd /home/shg047/oasis/DennisLo2015/fastq perl ../bismark.pbs.pl ../Sample_queue.txt
- mapping metrics summary:
perl ~/bin/bismarkMappingStatistic.pl
Bam to Hapinfo[edit]
- Bam merge (forget it, so I just use the run1):
Pregnancy.8.run1.read1.hapInfo.txt Pregnancy.8.run2.read1.hapInfo.txt Pregnancy.9.run1.read1.hapInfo.txt Pregnancy.9.run2.read1.hapInfo.txt
- Deduplicate to Bam files
deduplicate_bismark -s --bam CTR114_trimmed.fq.gz_bismark_bt2.bam # CTR114_trimmed.fq.gz_bismark_bt2.deduplicated.bam will be created
- Bam to hapinfo
cd /oasis/tscc/scratch/ddiep/DennisLo_WGBS_BAMfiles cd /home/shg047/oasis/DennisLo2015/hapinfo perl ~/bin/samInfoPrep4Bam2Hapinfo.pl /oasis/tscc/scratch/ddiep/DennisLo_WGBS_BAMfiles/ > saminfo.txt perl ~/bin/bam2hapInfo2PBS.pl saminfo.txt
- Dinh help me to finish the Bam File, At the same time, I also aligned them by myself again to check the difference.
cd /home/shg047/oasis/DennisLo2015/sortbam perl ~/bin/samInfoPrep4Bam2Hapinfo.pl ./ > ../Saminfo4bam2hapinfo.txt perl ~/bin/bam2hapInfo2PBS.V2016.pl ../Saminfo4bam2hapinfo.txt submit bismark
Hapinfo to MHL[edit]
cd /home/shg047/oasis/DennisLo2015/hapinfo perl ~/bin/hapinfo2mhl.pl ./ > ../dennis.mhl.march24.txt
Bam to MethyFreq[edit]
Methylation Haplotype Load[edit]
- Distribution in SamplesScatterPlot-File:6681.tm.png.R
*MHL:File:66F0.tm-mhl-dennislo.png MF:File:6681.tm.png MHLvsMFFile:7254.tm.png Hist:File:7BC8.tm.png
*MHL vs MF: File:3E18.tm.png * PileOMeth-MF vs Hapinfo-MF:File:46F2.tm.png