nanopore甲基化分析

[anneng]

https://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html
安装：速度可能比较慢 可以把仓库加载到码云
git clone --recursive https://github.com/jts/nanopolish.git
cd nanopolish
make
make过程会下载hdf5-1.8.14 可以直接用axel先加速下载再编译
预处理　将原始文件和fastq关联起来
nanopolish index -d fast5_files/ output.fastq

和参考序列进行比对：
minimap2 -a -x map-ont reference.fasta output.fastq | samtools sort -T tmp -o output.sorted.bam
samtools index output.sorted.bam
计算甲基化:
nanopolish call-methylation -t 8 -r output.fastq -b output.sorted.bam -g reference.fasta -w "chr20:5,000,000-10,000,000" > methylation_calls.tsv
统计：
scripts/calculate_methylation_frequency.py methylation_calls.tsv > methylation_frequency.tsv