Data processing steps.md

In fanyue322/IMAGE: Title: High-Powered Detection of Genetic Effects on DNA Methylation Using Integrated Methylation QTL Mapping and Allele-Specific Analysis

Data processing steps

1.Trimmed the adaptors in the fastq files using TrimGalore!

./trim_galore -a <adapter> --gzip --rrbs --length 15 --stringency 4 FILE

2.Mapped to the baboon reference genome using BSseeker2

python bs_seeker2-align.py -i FILE.fq --aligner=bowtie2 -o FILE.bam -g reference.fa -r 
python bs_seeker2-call_methylation.py -i FILE.bam -o FILE --db reference 

3.Called SNPs using CGmaptools with the BayesWC strategy

cgmaptools  snv -i FILE.ATCGmap.gz -m bayes -v FILE.vcf -o FILE.snv  –bayes-e=0.01 –bayes-dynamicP -a

4.Merged and filtered VCF files using VCFtools

vcftools --vcf FILE.vcf –minDP 3 --max-missing 0.5 --maf 0.05 --recode --recode-INFO-all  --out FILE

5.Called allele-specific methylation using CGmaptools

cgmaptools asm -r reference.fa -b FILE.bam -l FILE.vcf > FILE.asm

fanyue322/IMAGE documentation built on Jan. 30, 2020, 1:50 p.m.