Month: December 2020
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BS-seq分析流程(一)
短序列的质控都可以使用trimmomatic,这里不多做介绍,得到的clean data可做下面分析 一、比对和甲基化位点提取(Bismark) Bismark安装及使用 git clone https://github.com/FelixKrueger/Bismark.git #conda install -c bioconda bismark #Genome Preparation /opt/biosoft/Bismark-0.23.0/bismark_genome_preparation –parallel 40 –verbose ./ #bismark alignment for i in `cat ../samples.txt` do echo “/opt/biosoft/Bismark-0.23.0/bismark –parallel 40 –genome ./ –phred33-quals -1 ../$i.1.fastq -2 ../$i.2.fastq” done > bismark.list ParaFly -c bismark.list -CPU 4 #deduplicate for i in `cat ../samples.txt` do echo “/opt/biosoft/Bismark-0.23.0/deduplicate_bismark…
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ATAC-seq分析流程(一)
首先根据今年发表在Genome Biology上一篇综述总览分析流程: 作者建议的预处理分析流程为:FastQC-trimmomatic-BWA-MEM-ATACseqQC。 一、使用Fastqc对fastq 文件的测序质量统计 for i in `ls *fastq`; do echo “fastqc -t 4 -o ./ $i”; done > fastqc.sh nohup ParaFly -c fastqc.sh -CPU 18 & 二、Trimmomatic质控(可使用 cutadapt,AdapterRemoval v2,Skewer 和 trimmomatic 等软件) The forward and reverse adapters are slightly different. We will also trim low quality bases at the ends of the reads…