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

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>Shicheng
>Shicheng
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*Fastq donwload address: [[File:Haib.download.files.txt]]
*Fastq donwload address: [[File:Haib.download.files.txt]]
  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===
===Fastq Quality Control===

Revision as of 08:54, 7 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

Fastq Alignment

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

Methylation haploinfo

Methylation Haplotype Load Matrix

Evaluation of the data quality

Merge with our RRBS data