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
- fastq file: shg047@genome-miner.ucsd:/media/TmpStore1/DennisLo2015
- Readme: File:DennisLo2015-Readme.txt
- bam file:
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