Question: Removing sequences originated from repetitive regions from FASTQ
0
gravatar for geek_y
5.1 years ago by
geek_y9.7k
Barcelona/CRG/London/Imperial
geek_y9.7k wrote:

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 ?

 

paralogs fastq • 1.4k views
ADD COMMENTlink modified 5.1 years ago by Prakki Rama2.3k • written 5.1 years ago by geek_y9.7k

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

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by Ido Tamir5.0k
0
gravatar for Prakki Rama
5.1 years ago by
Prakki Rama2.3k
Singapore
Prakki Rama2.3k wrote:

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.

ADD COMMENTlink written 5.1 years ago by Prakki Rama2.3k
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