-
Presumably now is the right time to build into Atlas the policy of ignoring kmers in an allele which we know exist elsewhere in the genome
-
Hello! Thanks for your powerful tool!
I have a question about the detected site, is there any way to know that the modification type? Let's say we have several NNGNN kmers, then can we know whethe…
-
Would an option to ignore over-occurring kmers make mash more robust against large repeat families and multi-copy plasmids?
mash estimates the coverage in -r mode, and it uses -m for a min freq, bu…
-
I want to generate a db of all kmers and their counts for a reference genome using `meryl count`, then for thousands of small (~1-5 kbp) sequences I want to extract all kmers and find their counts in …
-
just curious,
is it possible implement something similar for trna search?
my interest : “missing” trna anticodons.
see
https://pmc.ncbi.nlm.nih.gov/articles/PMC8007984/
-
Hi Kivanc,
I've updated kGWASflow and tried to run the analysis including aligning the kmers. Unfortunately, generating the Manhattan plot yields errors, with unhelpful logs:
```
y_max: 19.2846…
-
Hi, I'm trying to run the flow via snakemake (snakemake --cores all --use-conda ) but I get this error.
https://raw.githubusercontent.com/akcorut/kGWASflow/v1.3.0/workflow/rules/common.smk:98: Sy…
-
HAWK has apparently run successfully on my data and I have an interesting case_kmers.fasta file that I could assemble with ABYSS.
However, no control_kmers.fasta file was produced.
Any thoughts on w…
-
Hi Jellyfish group,
I am trying to use jellyfish to generate kmer for a complete genome (~14G). I accidentally found some kmers should be in the genome but are not showing in the final txt file aft…
-
Rethinking regarding the chunk size, should we define the chunk size as the number of sequences or the number of kmers?
Chunk size as the number of sequences should work when the sequence lengths a…