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No best K value found

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?

assembly kmergenie
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updated by shaileshdesai76 • shaileshdesai76 • written by kspata kspata

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.

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written by Brian Bushnell Brian Bushnell

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

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written by Rayan Chikhi Rayan Chikhi

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

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written by kspata kspata

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.

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written by karl.stamm karl.stamm

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.

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written by kspata kspata

how did you install r, like where ? did you install r in root and kmergenie in other folder ? i am facing same problem ?

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written by shaileshdesai76 • shaileshdesai76

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