Hi there I wish to ask a basic question to which I really didn't find an answer to. Please guide me.
I have 250 bp read length deep seq data. I wish to run Error Correction tools on it like SOAP Error Corrector or Quake. All of these programs ask for a kmer value. Even Jellyfish asks for a kmer value to estimate genome size.
Now I used kmergenie to find the optimum kmer value which I guess I did wrong because my kmer value exceeds 180. Please correct me if I am wrong but this 180 value I got would be ideal for a de-novo ASSEMBLY right? Error correction would need a much shorter kmer value.
In many research papers I have read they have assigned a kmer value like 17, 21, 23 and so on. This is for 150 bp reads. I just want to know where they got these values from. What should I use if i have 250 bp reads?