Ns126:DennisLo2015-PNAS: Difference between revisions

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>Shicheng
>Shicheng
Line 36: Line 36:
  cd /home/shg047/oasis/DennisLo2015/fastq
  cd /home/shg047/oasis/DennisLo2015/fastq
  perl ../bismark.pbs.pl ../Sample_queue.txt
  perl ../bismark.pbs.pl ../Sample_queue.txt
=== Bam to Hapinfo ===
cd /oasis/tscc/scratch/ddiep/DennisLo_WGBS_BAMfiles
perl ~/
=== Hapinfo to MHL ===
=== Bam to MethyFreq===

Revision as of 02:11, 16 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


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
perl ~/

Hapinfo to MHL

Bam to MethyFreq