Xiao-Ou Zhang

Thanks a lot. I will try it later.

It works. I haven't find any bugs. Thanks a lot.

Cool! Seem like they try to split Zim into different repos. See https://github.com/zimframework/zim/issues/2 !

Because the owner of prezto has disappeared for long time, prezto also plans to move to new repos. See https://github.com/sorin-ionescu/prezto/issues/1239.

We did not set filters on the name of chromosomes. Theoretically, if your gene annotations contain mitochondrial genes, it can report mitochondrial circRNAs.

Please make sure `/home/jaber/Desktop/volox/tophat2/accepted_hits.bam` is the BAM file produced by TopHat-Fusion.

Please refer to the [CIRCexplorer2 manual](https://circexplorer2.readthedocs.io/en/latest/tutorial/setup/).

I recommend using STAR to align circRNAs and skipping the assembly step to speed up your process.

You can use STAR with stringtie to assemble and denovo to get novel circRNAs. You just neet to offer CIRCexplorer2 with the gene annotation file assembled using stringtie.

If you want to use BAM files from STAR alignment, it requires chimeric alignment (set `--chimSegmentMin` in STAR) for CIRCexplorer2 to identify circRNA junction reads.