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Interpreting Tallymer search output
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k-mer counters - presence/absence matrix
written by lizabe 1Hi all, I need to compute a presence/absence matrix (binary) of k-mers present in a set of genomes (fasta files). Could you please suggest me …
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Jellyfish: every other kmer count is zero
written by Lina F 20Hi all, I found a tutorial suggesting how to use Jellyfish to estimate genome size: http://koke.asrc.kanazawa-u.ac.jp/HOWTO/kmer-genomesize.html However, after running `jellyfish count` and `jellyfish histo` the …
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Estimate the genome heterozygosity from a PacBio dataset
written by gabri 6Hi! I know that in the case of Illumina sequences it is possible to use jellyfish for the k-mers count, using short sequences and the …
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More specifics on Jellyfish -C methodology.
written by dlawre14 3I know in Jellyfish `-C` stands for canonical kmers, however I'm a little iffy on how this is implemented. Does Jellyfish take into account whether …
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Jellyfish for transcriptome assembly
written by SJ Basu 6Hello, I have 2X150 reads of plant transcriptome and would like to assemble it using oases/velvet pipeline but I need to provide a kmer length …
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How do I count the number of nucleotides using jellyfish; can I obtain the number of nucleotides th…
written by Tom 2I have a comparison that's been puzzling me. Suppose I have a fastq file for a bacteria: rawread.fastq I do: `cat rawread.fastq | awk 'NR%4==2{print}' …
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Selecting sequences from a multi-fasta with certain kmers
written by michberr8 0Hi, I have a fasta file with about 30 9-mers. I also have some metagenomes in fasta format which are about 15 GB (~100 million …
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Jellyfish -C option explanation
written by pbigbig 25Hi, When working with Jellyfish, I used sample command in their guide: $ jellyfish count -m 22 -s 100M -t 16 -C merged.fq.gz and I …
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Any tools to count kmers in tumor/normal (contrast) pairs of samples?
written by 14134125465346445 361Are there any tools that would allow one to count the number of times a kmer is present in both samples of a pair of …