生信学习--使用circle-map提取eccDNA

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#下载bwa
wget https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2
#解压缩
tar -jxvf bwa-0.7.17.tar.bz2

#编译
cd bwa-0.7.17
make

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#尝试执行bwa
~/bwa-0.7.17/bwa

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Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188
Contact: Heng Li <lh3@sanger.ac.uk>
#…………省略多行

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#先回到家目录
cd ~
#下载samtools
wget https://github.com/samtools/samtools/releases/download/1.16.1/samtools-1.16.1.tar.bz2
#解压
tar jxvf samtools-1.16.1.tar.bz2

#安装
cd samtools-1.16.1
#注意configure时使用绝对路径
./configure --prefix=/home/user/samtools-1.16.1
make
make install

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~/samtools-1.16.1/samtools

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Program: samtools (Tools for alignments in the SAM format)
Version: 1.16.1 (using htslib 1.16)
#……………省略多行

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#回到家目录
cd ~
#下载anaconda
wget https://repo.anaconda.com/archive/Anaconda3-2022.05-Linux-x86_64.sh
#安装anaconda
sh Anaconda3-2022.05-Linux-x86_64.sh

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#创建虚拟环境
conda create --name circle-map
#激活虚拟环境
conda activate circle-map

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 conda install -c bioconda circle-map

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#清空.condarc文件中的内容
echo "" > ~/.condarc
#然后再将要替换的镜像添加到.condarc中
echo "channels:
  - defaults
  - conda-forge
show_channel_urls: true
default_channels:
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2
custom_channels:
  conda-forge: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  msys2: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  bioconda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  menpo: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  pytorch: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  pytorch-lts: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  simpleitk: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud" > ~/.condarc
  #若上一步安装circle-map失败接着执行
  conda install -c bioconda circle-map

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Circle-Map -h

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wget https://raw.githubusercontent.com/iprada/Circle-Map/master/tutorial/unknown_circle_reads_1.fastq
wget https://raw.githubusercontent.com/iprada/Circle-Map/master/tutorial/unknown_circle_reads_2.fastq

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#下载参考基因组
wget -c ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
#文件名有点长，可以修改一下文件名
mv GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz hg38.fna.gz
#解压参考基因组
gunzip -d hg38.fna.gz

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~/bwa-0.7.17/bwa index hg38.fna.gz
~/samtools-1.16.1/samtools faidx hg38.fna

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#创建一个脚本文件
vim circle_extract_test.sh

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#!/bin/bash
conda activate circle-map
~/bwa-0.7.17/bwa mem -q hg38.fna unknown_circle_reads_1.fastq unknown_circle_reads_2.fastq > unknown_circle.sam
~/samtools-1.16.1/samtools sort -n -o qname_unknown_circle.bam unknown_circle.sam
~/samtools-1.16.1/samtools sort -o sorted_unknown_circle.bam unknown_circle.sam
Circle-Map ReadExtractor -i qname_unknown_circle.bam -o circular_read_candidates.bam
~/samtools-1.16.1/samtools sort -o sort_circular_read_candidates.bam circular_read_candidates.bam
~/samtools-1.16.1/samtools index sort_circular_read_candidates.bam
~/samtools-1.16.1/samtools index sorted_unknown_circle.bam
Circle-Map Realign -i sort_circular_read_candidates.bam -qbam qname_unknown_circle.bam -sbam sorted_unknown_circle.bam -fasta hg38.fna -o my_unknown_circle.bed

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chmod +x circle_extract_test.sh

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./circle_extract_test.sh

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less -S my_unknown_circle.bed