Ns126:DennisLo2015-PNAS: Difference between revisions
Jump to navigation
Jump to search
>Shicheng |
>Shicheng |
||
Line 65: | Line 65: | ||
=== Methylation Haplotype Load === | === Methylation Haplotype Load === | ||
* Distribution in Samples | * Distribution in Samples | ||
*[[File: | *[[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
- fastq file: shg047@genome-miner.ucsd:/media/TmpStore1/DennisLo2015
- Readme: File:DennisLo2015-Readme.txt
- bam file:
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