Deleted:CircRNA extraction from bulk RNA seq datasets using CIRCexplorer2 with STAR alignment

Question

[choijamtsm]

Hello there, I newbie in bioinformatics,

I tried to extract circular RNA from bulk RNA sequencing datasets using CIRCexplorer2 with STAR alignment tools. I followed below tutorial.

https://circexplorer2.readthedocs.io/en/latest/tutorial/assembly/

But the problem occured until assembly part. Here they only used tophat tools. (which I dont plan to prefer to use it)

CIRCexplorer2 assemble -r mm10_ref_all.txt -m tophat -o assemble > CIRCexplorer2_assemble.log

So, to avoid using tophat, I used STAR tools command:

STAR --chimSegmentMin 10 --runThreadN 16 --runMode alignReads --quantMode GeneCounts --genomeDir some_dir --readFilesIn control_1.fastq control_1.2.fastq 

it gives me output of ReadsPerGene.out.tab and circularRNA_known.txt. But most of the identified circRNA has not counts number.

What shoud I do, in this situation? Thank you