Ns126:DennisLo2015-PNAS: Difference between revisions

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=== Methylation Haplotype Load ===
=== Methylation Haplotype Load ===
* Distribution in Samples
* Distribution in Samples
  *[[File:2AD9.tm.png|400px]]
  *[[File:66F0.tm-mhl-dennislo.png]] [[File:6681.tm.png]]

Revision as of 17:07, 28 March 2016

Motivation and Discovery

Data Introduction

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

  • 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

Trim_galore

  • 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
  • md5sum
md5sum *gz > md5sum.bak
DennisLo's trimed fastq md5sum

Bismark Alignment

  • 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

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's 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

cd /home/shg047/oasis/DennisLo2015/hapinfo
perl ~/bin/hapinfo2mhl.pl ./ > ../dennis.mhl.march24.txt

Bam to MethyFreq

Methylation Haplotype Load

  • Distribution in Samples
*File:66F0.tm-mhl-dennislo.png File:6681.tm.png