Ns126:DennisLo2015-PNAS

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Revision as of 18:22, 16 March 2016 by >Shicheng (→‎Data Storage)
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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

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

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

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

Hapinfo to MHL

Bam to MethyFreq