Ns126:DennisLo2015-PNAS: Difference between revisions

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>Shicheng
>Shicheng
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===Data Introduction===
===Data Introduction===


*Samples included:
* 94 Samples included:
  1) Normal pregnancies (15 sample, paired-end)
  1) Normal pregnancies (15 sample, paired-end)
  2) Organ transplantation patients (7 samples, paired-end)
  2) Organ transplantation patients (7 samples, paired-end)
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  5) Hepatocellular carcinoma (HCC) patient samples (29 samples, single-end)
  5) Hepatocellular carcinoma (HCC) patient samples (29 samples, single-end)
  6) Lymphoma case (4 sample, paired-end, multiple sequencing runs)
  6) Lymphoma case (4 sample, paired-end, multiple sequencing runs)
===Data Storage===
===Data Storage===
*Data Download
*Data Download

Revision as of 22:04, 15 March 2016

Motivation and Discovery

Data Introduction

  • 94 Samples included:
1) Normal pregnancies (15 sample, paired-end)
2) Organ transplantation patients (7 samples, paired-end)
3) Pregnancies with trisomy 21 fetus (5 samples, paired-end) 
4) Healthy control plasma samples (32 samples, single-end)
5) Hepatocellular carcinoma (HCC) patient samples (29 samples, single-end)
6) Lymphoma case (4 sample, paired-end, multiple sequencing runs)

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

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