Ns126:Calendar/NOTES/2016-1-5

From ZhangLabWiki
Revision as of 09:31, 7 January 2016 by >Shicheng (→‎Methylation haploinfo)
Jump to navigation Jump to search

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

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

Evaluation of the data quality

Merge with our RRBS data