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===Data Description=== | ===Data Description=== | ||
*RRBS Protocol: [[File:Myers Lab RRBS Protocol 6-18-2010.pdf]] | |||
*RRBS Analysis Protocol: [[File:RRBS Guide-Baraham.pdf]] | |||
*Normal tissues from RRBS data were downloaded from the ENCODE USCS genome browser [1]. Raw sequence data from 16 tissues were collected (Supplementary Table). Sequences were mapped to the bisulfite-converted human genome (NCBI hg19) using Bismark [2], after trimming the first three nucleotides, using the following parameters: --bowtie2 --phred64-quals --fastq -L 20 -N 1. | |||
*1.RRBS and ENCODE, http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethylRrbs/. | |||
*2.Krueger, F. and S.R. Andrews, Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 2011. 27(11): p. 1571-2. | |||
* Main important tissues were selected and merge to prediction model | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''ENCFF000LWX''' | |||
| align="center" style="background:#f0f0f0;"|'''RRBS''' | |||
| align="center" style="background:#f0f0f0;"|'''uterus''' | |||
| align="center" style="background:#f0f0f0;"|'''adult''' | |||
| align="center" style="background:#f0f0f0;"|'''female''' | |||
| align="center" style="background:#f0f0f0;"|'''44 year''' | |||
| align="center" style="background:#f0f0f0;"|'''36bp''' | |||
| align="center" style="background:#f0f0f0;"|'''Illumina Genome Analyzer IIx''' | |||
|- | |||
| ENCFF000LXB||RRBS||uterus||adult||female||44 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LVO||RRBS||lung||adult||female||83 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LVR||RRBS||lung||adult||female||83 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LVA||RRBS||kidney||adult||female||83 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LVB||RRBS||kidney||adult||female||83 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LUT||RRBS||breast||adult||female||21 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LUV||RRBS||breast||adult||female||21 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LUQ||RRBS||brain||adult||male||66 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LUU||RRBS||brain||adult||male||66 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LWS||RRBS||stomach||adult||female||83 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LWW||RRBS||stomach||adult||female||83 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LVU||RRBS||pancreas||adult||male||71 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LVW||RRBS||pancreas||adult||male||71 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LWO||RRBS||zone of skin||adult||female||83 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LWP||RRBS||zone of skin||adult||female||83 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LVI||RRBS||mononuclear cell||adult||unknown||54 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LVK||RRBS||mononuclear cell||adult||unknown||54 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LVJ||RRBS||liver||adult||female||83 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| ENCFF000LVN||RRBS||liver||adult||female||83 year||36bp||Illumina Genome Analyzer IIx | |||
|- | |||
| | |||
|} | |||
===Fastq Download=== | ===Fastq Download=== | ||
*Fastq donwload address: [[File:Haib.download.files.txt]] | *Fastq donwload address: [[File:Haib.download.files.txt]] | ||
* Sample Information:[[excel]] | |||
xargs -n 1 curl -O -L < haib.download.files.txt | xargs -n 1 curl -O -L < haib.download.files.txt | ||
===Check Phred Score=== | |||
perl ~/bin/checkphred.pl *fastq | |||
===Fastq Quality Control=== | |||
*trim_galore can used gz compressed fastq file as the input (so as the bismark) | |||
# trim_galore --phred64 --fastqc --illumina --non_directional --rrbs *.fastq | |||
trim_galore --phred64 --fastqc --illumina --rrbs *.fastq | |||
===Fastq Alignment=== | ===Fastq Alignment=== | ||
* bismark can used gz compressed fastq file as the input (so as the trim_galore) | |||
bismark --bowtie2 --phred64-quals --fastq -L 30 -N 1 /home/shg047/db/aligndb/hg19/bismark -1 ENCFF000MLM_trimmed.fq -o ../bam | |||
===Methylation haploinfo=== | |||
bismark_methylation_extractor \ | |||
--single-end \ | |||
--bedGraph \ | |||
--buffer_size 2G \ | |||
--remove_spaces \ | |||
--zero_based \ | |||
--merge_non_CpG \ | |||
--comprehensive \ | |||
--output ../methyfreq \ | |||
ENCFF000MLM_trimmed.fq_bismark_bt2.bam | |||
bismark_methylation_extractor --single-end --bedGraph --buffer_size 2G --remove_spaces --zero_based --merge_non_CpG --comprehensive --output ../methyfreq ENCFF000MLM_trimmed.fq_bismark_bt2.bam | |||
===Methylfreq Data Output=== | |||
* Bismark Run Perl Beginning Script | |||
#/usr/bin/perl | |||
use strict; | |||
use Cwd; | |||
my $dir=getcwd; | |||
chdir $dir; | |||
my @file=glob("*.fastq"); | |||
foreach my $file(@file){ | |||
open OUT,">$file.bismark.sh"; | |||
print OUT "cd $dir\n"; | |||
chomp(my $phredcheck=`perl /home/shg047/bin/checkphred.pl $file`); | |||
my ($phred)=split /\s+/,$phredcheck; | |||
my $phred="--phred$phred"; | |||
print OUT "trim_galore $phred --fastqc --illumina --non_directional --rrbs $file\n"; | |||
print OUT "bismark --bowtie2 --phred64-quals --fastq -L 30 -N 1 /home/shg047/db/aligndb/hg19/bismark -1 $file\_qual_trimmed.fastq -o ../bam\n"; | |||
print OUT "bismark_methylation_extractor --single-end --bedGraph --buffer_size 2G --remove_spaces --zero_based --merge_non_CpG --comprehensive -- output ../me | |||
} | |||
*Bismark Alignment Information Collection Script | |||
** Mapping efficency: [[File:BismarkAlignment.txt]] | |||
===Methylation Haplotype Load Matrix=== | ===Methylation Haplotype Load Matrix=== | ||
* methylation haplotype load for Haib data were save in TSCC | |||
/home/shg047/oasis/Haib/haploinfo/methHapLoad.matrix.txt | |||
===Methylation frequency Load Matrix=== | |||
* merge zero-based methylation cov files. | |||
#!/bin/csh | |||
#PBS -q pdafm | |||
#PBS -l nodes=1:ppn=1 | |||
#PBS -l walltime=1:00:00 | |||
#PBS -V | |||
#PBS -M shihcheng.guo@gmail.com | |||
#PBS -m abe | |||
#PBS -A k4zhang-group | |||
perl methylfreq2matrix.pl | |||
===Evaluation of the data quality=== | |||
* cluster analysis | |||
===Merge with our RRBS data=== | ===Merge with our RRBS data=== | ||
* data were saved in | |||
/home/shg047/oasis/monod/2016/monod.merge.wgbs.rrbs.txt |
Latest revision as of 21:54, 19 January 2016
Collection RRBS Dataset From Richard Myers, HAIB (Encode Project)[edit]
Data Description[edit]
- RRBS Protocol: File:Myers Lab RRBS Protocol 6-18-2010.pdf
- RRBS Analysis Protocol: File:RRBS Guide-Baraham.pdf
- Normal tissues from RRBS data were downloaded from the ENCODE USCS genome browser [1]. Raw sequence data from 16 tissues were collected (Supplementary Table). Sequences were mapped to the bisulfite-converted human genome (NCBI hg19) using Bismark [2], after trimming the first three nucleotides, using the following parameters: --bowtie2 --phred64-quals --fastq -L 20 -N 1.
- 1.RRBS and ENCODE, http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethylRrbs/.
- 2.Krueger, F. and S.R. Andrews, Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 2011. 27(11): p. 1571-2.
- Main important tissues were selected and merge to prediction model
ENCFF000LWX | RRBS | uterus | adult | female | 44 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LXB | RRBS | uterus | adult | female | 44 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LVO | RRBS | lung | adult | female | 83 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LVR | RRBS | lung | adult | female | 83 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LVA | RRBS | kidney | adult | female | 83 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LVB | RRBS | kidney | adult | female | 83 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LUT | RRBS | breast | adult | female | 21 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LUV | RRBS | breast | adult | female | 21 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LUQ | RRBS | brain | adult | male | 66 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LUU | RRBS | brain | adult | male | 66 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LWS | RRBS | stomach | adult | female | 83 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LWW | RRBS | stomach | adult | female | 83 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LVU | RRBS | pancreas | adult | male | 71 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LVW | RRBS | pancreas | adult | male | 71 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LWO | RRBS | zone of skin | adult | female | 83 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LWP | RRBS | zone of skin | adult | female | 83 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LVI | RRBS | mononuclear cell | adult | unknown | 54 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LVK | RRBS | mononuclear cell | adult | unknown | 54 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LVJ | RRBS | liver | adult | female | 83 year | 36bp | Illumina Genome Analyzer IIx |
ENCFF000LVN | RRBS | liver | adult | female | 83 year | 36bp | Illumina Genome Analyzer IIx |
Fastq Download[edit]
- Fastq donwload address: File:Haib.download.files.txt
- Sample Information:excel
xargs -n 1 curl -O -L < haib.download.files.txt
Check Phred Score[edit]
perl ~/bin/checkphred.pl *fastq
Fastq Quality Control[edit]
- trim_galore can used gz compressed fastq file as the input (so as the bismark)
# trim_galore --phred64 --fastqc --illumina --non_directional --rrbs *.fastq trim_galore --phred64 --fastqc --illumina --rrbs *.fastq
Fastq Alignment[edit]
- bismark can used gz compressed fastq file as the input (so as the trim_galore)
bismark --bowtie2 --phred64-quals --fastq -L 30 -N 1 /home/shg047/db/aligndb/hg19/bismark -1 ENCFF000MLM_trimmed.fq -o ../bam
Methylation haploinfo[edit]
bismark_methylation_extractor \ --single-end \ --bedGraph \ --buffer_size 2G \ --remove_spaces \ --zero_based \ --merge_non_CpG \ --comprehensive \ --output ../methyfreq \ ENCFF000MLM_trimmed.fq_bismark_bt2.bam
bismark_methylation_extractor --single-end --bedGraph --buffer_size 2G --remove_spaces --zero_based --merge_non_CpG --comprehensive --output ../methyfreq ENCFF000MLM_trimmed.fq_bismark_bt2.bam
Methylfreq Data Output[edit]
- Bismark Run Perl Beginning Script
#/usr/bin/perl use strict; use Cwd; my $dir=getcwd; chdir $dir; my @file=glob("*.fastq"); foreach my $file(@file){ open OUT,">$file.bismark.sh"; print OUT "cd $dir\n"; chomp(my $phredcheck=`perl /home/shg047/bin/checkphred.pl $file`); my ($phred)=split /\s+/,$phredcheck; my $phred="--phred$phred"; print OUT "trim_galore $phred --fastqc --illumina --non_directional --rrbs $file\n"; print OUT "bismark --bowtie2 --phred64-quals --fastq -L 30 -N 1 /home/shg047/db/aligndb/hg19/bismark -1 $file\_qual_trimmed.fastq -o ../bam\n"; print OUT "bismark_methylation_extractor --single-end --bedGraph --buffer_size 2G --remove_spaces --zero_based --merge_non_CpG --comprehensive -- output ../me }
- Bismark Alignment Information Collection Script
- Mapping efficency: File:BismarkAlignment.txt
Methylation Haplotype Load Matrix[edit]
- methylation haplotype load for Haib data were save in TSCC
/home/shg047/oasis/Haib/haploinfo/methHapLoad.matrix.txt
Methylation frequency Load Matrix[edit]
- merge zero-based methylation cov files.
#!/bin/csh #PBS -q pdafm #PBS -l nodes=1:ppn=1 #PBS -l walltime=1:00:00 #PBS -V #PBS -M shihcheng.guo@gmail.com #PBS -m abe #PBS -A k4zhang-group perl methylfreq2matrix.pl
Evaluation of the data quality[edit]
- cluster analysis
Merge with our RRBS data[edit]
- data were saved in
/home/shg047/oasis/monod/2016/monod.merge.wgbs.rrbs.txt