circle-map鉴定eccDNA--初步尝试

[ixxmu]

https://mp.weixin.qq.com/s/fLmnAP6XXFNJ_-vr5ey0dg

[github-actions[bot]]

circle-map鉴定eccDNA--初步尝试 by 东林的扯淡小屋

数据下载：

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

但是不太能够下载，还是直接将链接复制到浏览器直接打开然后保存吧。

软件下载：

conda create --name circle-map python=3.7#source activate circle-mapconda activate circle-map#Installation using conda: conda install -c bioconda circle-map

准备参考基因组：

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gzgunzip -d hg38.fa.gzbwa index hg38.fasamtools faidx hg38.fa

bwa mem -q /data/yudonglin/reference/human/hg38/hg38.fa unknown_circle_reads_1.fastq unknown_circle_reads_2.fastq > unknown_circle.sam
bwa mem -q /data/yudonglin/reference/human/hg19/bwa/hg19.fa unknown_circle_reads_1.fastq unknown_circle_reads_2.fastq > unknown_circle.sam

准备相关文件：

samtools sort -n -o qname_unknown_circle.bam unknown_circle.samsamtools sort -o sorted_unknown_circle.bam unknown_circle.sam

Circle-Map ReadExtractor -i qname_unknown_circle.bam -o circular_read_candidates.bamsamtools sort -o sort_circular_read_candidates.bam circular_read_candidates.bamsamtools index sort_circular_read_candidates.bamsamtools index sorted_unknown_circle.bamsamtools index qname_unknown_circle.bam

出了问题：conda install biopython=1.68

检测eccDNA：

Circle-Map Realign -i sort_circular_read_candidates.bam -qbam qname_unknown_circle.bam -sbam sorted_unknown_circle.bam -fasta /data/yudonglin/reference/human/hg19/bwa/hg19.fa -o my_unknown_circle.bed

报错，不然会应该有如下结果：

换为hg38就成功了，看来基因组不能随便选。

bwa mem -q /data/yudonglin/reference/human/hg38/hg38.fa unknown_circle_reads_1.fastq unknown_circle_reads_2.fastq > unknown_circle.samsamtools sort -n -o qname_unknown_circle.bam unknown_circle.samsamtools sort -o sorted_unknown_circle.bam unknown_circle.samCircle-Map ReadExtractor -i qname_unknown_circle.bam -o circular_read_candidates.bamsamtools sort -o sort_circular_read_candidates.bam circular_read_candidates.bamsamtools index sort_circular_read_candidates.bamsamtools index sorted_unknown_circle.bamCircle-Map Realign -i sort_circular_read_candidates.bam -qbam qname_unknown_circle.bam -sbam sorted_unknown_circle.bam -fasta /data/yudonglin/reference/human/hg38/hg38.fa -o my_unknown_circle.bed

参考资料：

https://github.com/iprada/Circle-Map/wiki/Tutorial:-Identification-of-circular-DNA-using-Circle-Map-Realign