Question: best kmer for genome size estimation
0
gravatar for popayekid55
8 months ago by
popayekid5540
popayekid5540 wrote:

Hi,

How do i select a best kmer for genome size estimation using jellyfish. I did using 31 and 41 both gave me a different result. Read chemistry is 150*2. are there any other tools, i am trying gce also.

Thanks in advance

kmer genome • 685 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by popayekid5540
1
gravatar for toralmanvar
8 months ago by
toralmanvar510
toralmanvar510 wrote:

Hello,

You can give a try to kmergenie.

Mostly it works for me.

ADD COMMENTlink written 8 months ago by toralmanvar510

I have tried that and best kmer from kmergenie was way too high. For this data it was 119. I was not sure this kmer to use in jellyfish for genome estimation

ADD REPLYlink written 8 months ago by popayekid5540

I don't understand when kmergenie along with best kmer already gives you estimated genome size then why you want to use jellyfish again for the same? Checking the histo.pdf file generated from kmergenie properly can give you required answer.

ADD REPLYlink written 8 months ago by toralmanvar510
1
gravatar for genomax
8 months ago by
genomax54k
United States
genomax54k wrote:

You can use Jellyfish as described here. BBMap suite has kmercountexact.sh that can be used for this purpose.

ADD COMMENTlink written 8 months ago by genomax54k

Thank you for the response. I was following the 1st link for genome estimation. It was mentioned for eukaryote 17-31 would be fine in jellyfish. In the tutorial they chose 25. Still not understanding how to choose the kmer length for counting. kmercountexact.sh is taking kmer length of 31 as default.

Is 31 a std kmer length for any eukaryote genomes?

ADD REPLYlink written 8 months ago by popayekid5540
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