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If the read name containing each can be found, I think jellyfish can be used to do more creative work, rather than just counting kmer, e.g. remove reads with some high occurrence kmer.
bzvew updated
6 years ago
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Presented the ChIP-seq peaks vs flanks comparison on Friday ENCODE call today. Jeff and Jacob suggest that HashingVectorizer is not a good comparator for my method since I want something that takes p…
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per our last R01 submission,
>We will implement amino acid and Dayhoff-6 queries with spacegraphcats by building secondary indices on top of the cDBG unitigs, which will allow us to anchor protein …
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Hello there!
I'm interested in using `khmer` to count and filter kmers from transcriptome datasets and then use the raw kmer counts across multiple (~10) samples as the "X" matrix for a classificatio…
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This issue is part of a series of issues to design the interface for collections across serial, parallel, and distributed contexts. Our goal is to determine what we think is reasonable to support and …
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### Background
Randstrobes is a method for linking two or more k-mers together into a seed that can be used for sequence mapping. I intend the below post to be a self-contained rough description of…
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I think the current default is 1e8, with 4 tables, which is 50MB.
At some point I calculated the number of protein k-mers in ENSEMBL human as ~4 x 10^7, so 10^8 is a pretty good upper bound, and …
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I want to sketch a genome to get 7-mers of amino-acids (ie peptides), so I give the new CLI a spin:
```bash
sourmash sketch translate -p k=7,k=10,scaled=1000,dayhoff genome.fasta
```
However, …
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Hi,
I am using SeqAn 2.3.2. I am following sequence I/O tutorial. The steps mentioned to read records in chunks is not very much clear. For example, I have a fastq file with 100 records. I am tryin…
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Strobealign currently uses [xxh64](https://github.com/ksahlin/strobealign/blob/8a0e047a451f4ff0ae74988f32695de0a0c80ea4/src/randstrobes.cpp#L38) to hash syncmers.
We could switch to a different, fa…