Ns126:Calendar/NOTES/2016-1-5: Difference between revisions

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*1.RRBS and ENCODE, http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethylRrbs/.
*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.
*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.
{| {{table}}
| ENCFF000LWX||RRBS||uterus||adult||female||44 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LXB||RRBS||uterus||adult||female||44 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LVO||RRBS||lung||adult||female||83 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LVR||RRBS||lung||adult||female||83 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LWH||RRBS||skeletal muscle tissue||adult||male||71 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LWK||RRBS||skeletal muscle tissue||adult||male||71 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000MLD||RRBS||islet of Langerhans||unknown||unknown||||36||Illumina Genome Analyzer IIx
|-
| ENCFF000MLE||RRBS||islet of Langerhans||unknown||unknown||||36||Illumina Genome Analyzer IIx
|-
| ENCFF000MLJ||RRBS||islet of Langerhans||unknown||unknown||||36||Illumina Genome Analyzer IIx
|-
| ENCFF000MLM||RRBS||islet of Langerhans||unknown||unknown||||36||Illumina Genome Analyzer IIx
|-
| ENCFF000MLP||RRBS||islet of Langerhans||unknown||unknown||||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LUN||RRBS||adrenal gland||adult||female||88 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LUP||RRBS||adrenal gland||adult||female||88 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LVA||RRBS||kidney||adult||female||83 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LVB||RRBS||kidney||adult||female||83 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LUT||RRBS||breast||adult||female||21 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LUV||RRBS||breast||adult||female||21 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LUQ||RRBS||brain||adult||male||66 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LUU||RRBS||brain||adult||male||66 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LVE||RRBS||heart left ventricle||adult||male||26 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LVF||RRBS||heart left ventricle||adult||male||26 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LWS||RRBS||stomach||adult||female||83 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LWW||RRBS||stomach||adult||female||83 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LVV||RRBS||pericardium||adult||female||70 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LWA||RRBS||pericardium||adult||female||70 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LVU||RRBS||pancreas||adult||male||71 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LVW||RRBS||pancreas||adult||male||71 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LWO||RRBS||zone of skin||adult||female||83 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LWP||RRBS||zone of skin||adult||female||83 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LVI||RRBS||mononuclear cell||adult||unknown||54 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LVK||RRBS||mononuclear cell||adult||unknown||54 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LVJ||RRBS||liver||adult||female||83 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LVN||RRBS||liver||adult||female||83 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LWD||RRBS||skeletal muscle tissue||adult||female||83 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LWL||RRBS||skeletal muscle tissue||adult||female||83 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LVZ||RRBS||placenta||adult||female||29 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LWE||RRBS||placenta||adult||female||29 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LWT||RRBS||testis||adult||male||41 year||36||Illumina Genome Analyzer IIx
|-
| ENCFF000LWY||RRBS||testis||adult||male||41 year||36||Illumina Genome Analyzer IIx
|-
|
|}


===Fastq Download===
===Fastq Download===

Revision as of 22:27, 12 January 2016

Collection RRBS Dataset From Richard Myers, HAIB (Encode Project)

Data Description

  • 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.
ENCFF000LWX RRBS uterus adult female 44 year 36 Illumina Genome Analyzer IIx
ENCFF000LXB RRBS uterus adult female 44 year 36 Illumina Genome Analyzer IIx
ENCFF000LVO RRBS lung adult female 83 year 36 Illumina Genome Analyzer IIx
ENCFF000LVR RRBS lung adult female 83 year 36 Illumina Genome Analyzer IIx
ENCFF000LWH RRBS skeletal muscle tissue adult male 71 year 36 Illumina Genome Analyzer IIx
ENCFF000LWK RRBS skeletal muscle tissue adult male 71 year 36 Illumina Genome Analyzer IIx
ENCFF000MLD RRBS islet of Langerhans unknown unknown 36 Illumina Genome Analyzer IIx
ENCFF000MLE RRBS islet of Langerhans unknown unknown 36 Illumina Genome Analyzer IIx
ENCFF000MLJ RRBS islet of Langerhans unknown unknown 36 Illumina Genome Analyzer IIx
ENCFF000MLM RRBS islet of Langerhans unknown unknown 36 Illumina Genome Analyzer IIx
ENCFF000MLP RRBS islet of Langerhans unknown unknown 36 Illumina Genome Analyzer IIx
ENCFF000LUN RRBS adrenal gland adult female 88 year 36 Illumina Genome Analyzer IIx
ENCFF000LUP RRBS adrenal gland adult female 88 year 36 Illumina Genome Analyzer IIx
ENCFF000LVA RRBS kidney adult female 83 year 36 Illumina Genome Analyzer IIx
ENCFF000LVB RRBS kidney adult female 83 year 36 Illumina Genome Analyzer IIx
ENCFF000LUT RRBS breast adult female 21 year 36 Illumina Genome Analyzer IIx
ENCFF000LUV RRBS breast adult female 21 year 36 Illumina Genome Analyzer IIx
ENCFF000LUQ RRBS brain adult male 66 year 36 Illumina Genome Analyzer IIx
ENCFF000LUU RRBS brain adult male 66 year 36 Illumina Genome Analyzer IIx
ENCFF000LVE RRBS heart left ventricle adult male 26 year 36 Illumina Genome Analyzer IIx
ENCFF000LVF RRBS heart left ventricle adult male 26 year 36 Illumina Genome Analyzer IIx
ENCFF000LWS RRBS stomach adult female 83 year 36 Illumina Genome Analyzer IIx
ENCFF000LWW RRBS stomach adult female 83 year 36 Illumina Genome Analyzer IIx
ENCFF000LVV RRBS pericardium adult female 70 year 36 Illumina Genome Analyzer IIx
ENCFF000LWA RRBS pericardium adult female 70 year 36 Illumina Genome Analyzer IIx
ENCFF000LVU RRBS pancreas adult male 71 year 36 Illumina Genome Analyzer IIx
ENCFF000LVW RRBS pancreas adult male 71 year 36 Illumina Genome Analyzer IIx
ENCFF000LWO RRBS zone of skin adult female 83 year 36 Illumina Genome Analyzer IIx
ENCFF000LWP RRBS zone of skin adult female 83 year 36 Illumina Genome Analyzer IIx
ENCFF000LVI RRBS mononuclear cell adult unknown 54 year 36 Illumina Genome Analyzer IIx
ENCFF000LVK RRBS mononuclear cell adult unknown 54 year 36 Illumina Genome Analyzer IIx
ENCFF000LVJ RRBS liver adult female 83 year 36 Illumina Genome Analyzer IIx
ENCFF000LVN RRBS liver adult female 83 year 36 Illumina Genome Analyzer IIx
ENCFF000LWD RRBS skeletal muscle tissue adult female 83 year 36 Illumina Genome Analyzer IIx
ENCFF000LWL RRBS skeletal muscle tissue adult female 83 year 36 Illumina Genome Analyzer IIx
ENCFF000LVZ RRBS placenta adult female 29 year 36 Illumina Genome Analyzer IIx
ENCFF000LWE RRBS placenta adult female 29 year 36 Illumina Genome Analyzer IIx
ENCFF000LWT RRBS testis adult male 41 year 36 Illumina Genome Analyzer IIx
ENCFF000LWY RRBS testis adult male 41 year 36 Illumina Genome Analyzer IIx

Fastq Download

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

  • 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
}

Methylation Haplotype Load Matrix

Evaluation of the data quality

Merge with our RRBS data