Ns126:DennisLo2015-PNAS: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Shicheng
>Shicheng
 
(26 intermediate revisions by the same user not shown)
Line 2: Line 2:


===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)
Line 30: Line 30:
  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
Line 48: Line 49:


=== 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
* above is Based on Dinh's Bam File, However, I don't have enough information about the alignment and pre-processing. Therefore I aligned them by myself again.  
* 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/bam
  cd /home/shg047/oasis/DennisLo2015/sortbam
  perl ~/bin/bam2hapInfo2PBS.pl ../Saminfo4bam2hapinfo.txt submit
perl ~/bin/samInfoPrep4Bam2Hapinfo.pl ./ > ../Saminfo4bam2hapinfo.txt
  perl ~/bin/[[bam2hapInfo2PBS.V2016.pl]] ../Saminfo4bam2hapinfo.txt submit bismark


=== Hapinfo to MHL ===
=== Hapinfo to MHL ===
cd /home/shg047/oasis/DennisLo2015/hapinfo
perl [[~/bin/hapinfo2mhl.pl]] ./ > ../dennis.mhl.march24.txt


=== Bam to MethyFreq===


 
=== Methylation Haplotype Load ===
=== Bam to MethyFreq===
* Distribution in Samples[[ScatterPlot-File:6681.tm.png.R]]
*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
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]

*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