Ns126:Calendar/NOTES/2016-1-5

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

Data Description

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 --phred64 --fastqc --illumina --non_directional --rrbs *.fastq

Fastq Alignment

bismark --bowtie2 --phred64-quals --non_directional --fastq -L 30 -N 1 /home/shg047/db/aligndb/hg19/bismark -1 ENCFF000LUN.fastq_qual_trimmed.fastq -o ../bam

Methylation haploinfo

bismark_methylation_extractor \
--single-end \
--bedGraph \
--buffer_size 2G \
--remove_spaces \
--zero_based \
--merge_non_CpG \
--comprehensive \
--output ../methyfreq \
ENCFF000LUN.fastq_qual_trimmed.fastq.bam
bismark_methylation_extractor --single-end --bedGraph --buffer_size 2G --remove_spaces --zero_based --merge_non_CpG --comprehensive --output ../methyfreq  ENCFF000LUN.fastq_qual_trimmed.fastq.bam

Methylation Haplotype Load Matrix

#/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 --non_directional --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
}

Evaluation of the data quality

Merge with our RRBS data