Does Jellyfish k-mer counting tool give wrong k-mers?

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3.1 years ago

rubyeat88 ▴ 10

I have just experienced a strange thing in Jellyfish. While counting k-mers using Jellyfish, some k-mers generated which is not in main DNA sequence but in dump.fa file. Isn't it strange? I also checked its reverse complement and surprisingly it is not in dump file. I couldn't get any idea how this k-mer generates?

software error • 1.2k views

ADD COMMENT • link 3.1 years ago by rubyeat88 ▴ 10

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Could you give the exact invocation of jellyfish? What is in the dump.fa file and where does it come from? And how did you check the presence or absence of the kmer in question?

ADD REPLY • link 3.1 years ago by Michael 54k

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jellyfish count -m 15 -s 300M -t 12 -C gorrila.fa -o gorrila_counts.jf; jellyfish dump gorrila_counts.jf > gorrila_counts_dumps.fa;

here I am using 15-ker for Gorrila sequence and the count of all k-mer is written in Gorrila counts dumps.fa file. Now when I was checking the k-mers manually in fasta file, I didn't get it and also the reverse complement. Then how this k-mer generates in dump file if it is not present in main sequence?

ADD REPLY • link 3.1 years ago by rubyeat88 ▴ 10

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