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

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


===Methylation haploinfo===
===Methylation haploinfo===

Revision as of 08:32, 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

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/hg19/meth/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