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

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===Methylfreq Data Output===
===Methylfreq Data Output===
 
* Bismark Run Perl Beginning Script
  #/usr/bin/perl
  #/usr/bin/perl
  use strict;
  use strict;
Line 56: Line 56:
  print OUT "bismark_methylation_extractor --single-end --bedGraph --buffer_size 2G --remove_spaces --zero_based --merge_non_CpG --comprehensive --  output ../me
  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===

Revision as of 22:42, 8 January 2016

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

Fastq Alignment

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