参考官方链接：

[[https://circexplorer2.readthedocs.io/en/latest/]]

第一步：通过bwa比对获得bam文件

<code>
export PYTHONPATH=""

unset PERL5LIB

export PATH=/TJPROJ2/GB/PUBLIC/software/GB_TR/mRNA/miniconda3/envs/CircNovel/bin:$PATH


bwa mem -t 4 -T 19 hg19.fa Y3_1.fq.gz Y3_2.fq.gz 1>bwa_out_Y3.sam 2>bwa_out_Y3.log
</code>
第二步：使用CIRCexplorer2 的parse和annotate的功能，进行circRNA鉴定。
<code>
/TJPROJ6/RNA_SH/personal_dir/fengjie/SOFTWARE/CONDA/conda/bin/CIRCexplorer2 parse -t BWA bwa_out_Y3.sam > CIRCexplorer2_parse.log2
/TJPROJ6/RNA_SH/personal_dir/fengjie/SOFTWARE/CONDA/conda/bin/CIRCexplorer2 annotate -g hg19.fa -r hg19_ref.txt -b back_spliced_junction.bed -o circularRNA_known.txt > CIRCexplorer2_annotate.log
</code>