I have to run CIRI on several fq files for the identification of circular RNA but realize that there is a small percentage of rRNA contaminants within them. know We did not remove the contamination before library construction earlier as protocol. Now that I have run hisat2 on files and CIRI on .sam for circular RNA identification. Is there a way to remove the contaminants? Thanks!

I'm not 100% clear on your objectives for filtering your data, but bbduk from BBMap can be used to remove reads from a fastq file that match to a set of user defined sequences (in your case, rRNA sequences).