Ns126:Calendar/NOTES/2016-1-5
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Collection RRBS Dataset From Richard Myers, HAIB (Encode Project)
Data Description
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 --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