More posts like this
-
How to choose k-mer for the genome size estimation?
written by 524730309 0Hi, there. I am using Jellyfish-2 and Genomescope2 to estimate the genome size of my object. I choose different k-mers (e.g. 17 and 21) and …
-
How to use a single file as the input to MaSuRCA
written by Kash 11Hi everyone, I generated k-mers of a certain region of my genome of interest using Jellyfish software. Next I extracted certain k-mers from the dump.fa …
-
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 …
-
Nothing happens when I type jellyfish histo mer_counts.jf - command fails to produce k-mer histogram
written by msimmer92 31Hello! I am doing RNA-seq analysis of human natural killer cells. I downloaded Jellyfish 2.2.6 to visualize k-mer content. The installation was the following using …
-
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 …
-
Getting sequence id from k-mers using jellyfish
written by Protostome 5I'm currently extracting a list of k-mers from a FastQ file, using jellyfish. In addition to the k-mers, I would also like a list of …
-
K-mers using JEllyfish
written by itsthegodzgarbage 1<p>Hi,</p> <p>I am trying to find all k-mers in my fasta files. For eg if the sequence is AAATTCCGGGGGAAAA , if I want all k-mers …
-
Anybody Has Experience In This Tool :Jellyfish? Need Help
written by GAO Yang 25<p>Hi, I was trying <a href="https://banana-slug.soe.ucsc.edu/bioinformatic_tools:jellyfish">Jellyfish</a> on some downloaded data: <a href="http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=ERA000206">Illumina-Ecoli<em>100</em>PE</a> and the data sequenced in our lab. But none of them showed the …
-
Tool: Jellyfish - Fast, Parallel K-Mer Counting For Dna
written by Istvan Albert 10KJELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of …
-
Is There A Fast Hashing Function For Nucleotide K-Mers (Q-Grams)?
written by Ketil 415<p>I would like to index all k-mers in a set of nucleotide sequences. I could use a generic string based hash function, but my experiments …