FastQC result and cleaning sequence

[Kawaccino]

Hello,
I need your help for the cleaning of a sequence. I got a big Fastq file issued from an illumina sequening and even if it was supposed to be cleaned before I got it, when I do a Fastqc test, I obtain in the overrepresented sequences category a long table with about 12 sequences of ribosomal RNA that have no hit as possible sources (I got hits when I blast them on the NCBI Site); they are all similar, it's just some bases of the sequences that vary. And I also got strange results like RNA PCR Primer and of course my adaptators. I got rid of the adaptators by a simple Cutadapt, but I still have the other overrepresented sequences. How can I eliminate them, cause I suppose that cutadapt is not adapted to do that, is it?
Thank you for all the answer you'll be able to give me.
K.

[dpryan]

Aside from adapter removal, I don't know that I'd worry about removing ribosomal sequences from the fastq files. Aligning is quick enough to not worry about those and you can filter them out of your GTF file if you want to ignore them downstream.

[Kawaccino]

Ok, thank you for your answer, I will let them in that case and deal with them later.