Question: No best K value found
0
gravatar for kspata
2.1 years ago by
kspata40
Chicago
kspata40 wrote:

I used command ./kmergenie <filename.fastq> running histogram estimation Setting maximum kmer length to: 251 bp computing histograms (from k=21 to k=121): ntCard wall-clock time over all k values: 0 seconds fitting model to histograms to estimate best k could not predict a best k value No best k found

Do i need to change the k value to less than 21? How can I obtain the best K value for my reads?

kmergenie assembly • 818 views
ADD COMMENTlink modified 2.0 years ago • written 2.1 years ago by kspata40
1

sorry for wrong response. well I did not install R which is a prerequisite for kmergenie. I installed it and ran the command make again.

ADD REPLYlink written 2.0 years ago by kspata40

If it took zero seconds, it appears that there was probably zero input, so you may want to examine the input file and make sure it was non-empty. That said, if you want to find the optimal kmer length for assembly, I suggest you read this post.

ADD REPLYlink written 2.1 years ago by Brian Bushnell16k

hi, can you please post the first 4 lines of your fastq file?

ADD REPLYlink written 2.1 years ago by Rayan Chikhi1.4k

Hi thanks for replying.. i did a minor mistake while installing the software.. now its working correctly

ADD REPLYlink written 2.0 years ago by kspata40
1

This is not an answer to the question. It's useless to anyone searching this problem to see that you fixed it without saying what happened. It would be courteous to tell us what was going wrong or what you found.

ADD REPLYlink written 2.0 years ago by karl.stamm3.4k
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