Ns126:Calendar/NOTES/2016-1-5
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Collection RRBS Dataset From Richard Myers, HAIB (Encode Project)
Data Description
RRBS Protocol: File:Myers Lab RRBS Protocol 6-18-2010.pdf
Fastq Download
- Fastq donwload address: File: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 --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
Methylfreq Data Output
#/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 }