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Hi Team,
Just wonder whether open syncmer could be another option (https://github.com/bluenote-1577/local-kmer-selection-results/blob/db4c5c686433fb09f8571da7ca11b355aaa28e30/src/seeding_methods.rs…
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At the moment Nanocompore reports all the positions bellow the pvalue threshold, but when a position is significant the adjacent kmers are often significant as well. Using a peak calling algorithm wou…
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I am having some trouble understanding GenomeTester4 version 4.2.16 (stable) functionality, notably with the kmer frequency thresholds. For example, I have two datasets A and B and am interested in km…
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Hello,
I ran Genomescope on a plant genome, however, the model did not converge even with a distinct peak present. Is there any solution for this?
The full results are here: http://genomescope.…
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When filtering reads, with -ci0 for the reads (i.e. keep all reads, even ones with no kmers from the db), no hard-masking at all seems to happen. @marekkokot
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I ran hypo like this (now with correct input):
hypo -d $HOME/deer_assemblies/releases/v02.1/ovi_v02.1.fasta \
-r @illumina_reads.fofn \
-b $HOME/deer_assemblies/releases/v02.1/alignments/ovi_…
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Hello,Our team is working on a project about the genome Blacklist of different species, which uses umap software to generate a mappability containing umap mappability files. I have encountered these t…
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See #32; I'm doing my own thing (limited time, specific goals) and will document here.
Goal: evaluate how many false k-mers can be dropped from RNAseq data sets using a combination of diginorm and lo…
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Correction:
Actually, all three produced different results.
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Hello,
I compared the outputs from DSK to the ones generated by [JellyFish](https://gi…
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Hello professors:
Thanks for providing such a good tool!
I got a issue when running yak qv, the message is shown below.
[M::yak_ch_restore_core] inserted 1145802121 k-mers, of which 1145…