Removing sequences originated from repetitive regions from FASTQ

Question

[GouthamAtla]

Hi,

I would like to know if there is any way to remove sequences that are originated from repetitive regions ( paralogs ) of the genome with out having reference genome?

[Ido Tamir]

There is a lot more repetitiveness in many genomes than paralogs.

Answer 1

[Prakki Rama]

I think without any reference, it is not going to be easy to find out if the read is from repeat region or not. I have not tested, but may be, you can try running CENSOR on your reads, which searches against a reference collection of repeats.