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Recent Replies
Answer: Merging genotyping array VCFs and then running kinship analysis
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Jeremy Leipzig
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if you already have VCF try https://github.com/brentp/somalier
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GenoMax
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https://www.biostars.org/p/104936/<br>
https://www.biostars.org/p/148322/<br>
Comment: Adding new taxa to a Kraken2 db
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Hi Mark,
thanks for replying. Is it not what I have done? I have downloaded the genomes and added them to the db. Can you please be more s…
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Can you give an example of what you mean by swiss-prot file? I think you're describing a fasta file with amino acids. In that case use BioP…
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I wrote a simple and not elegant script (for 8 samples), maybe it will help someone.
>import pandas as pd
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You can not add genomes to an existing, precomputed kraken db. You have to download the plant genomes, add the new genomes then recreate th…
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Can you post an example of the vcf file you're working on?
In a vcf file, you should have the genotype which you can use to filter/count …
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To be honest, this sounds like a homework exercise...
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I did not know that 3.1 years ago. Thanks !
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thank you so much!
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You may also be able to get past this error by using the WAG matrix instead of LG, and in that case you could leave the other parameters as…
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Remove the version numbers using directions here and it should work: https://www.biostars.org/p/302441/#302485
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Well, kinda :) What Genozip does is uncompress the existing compression and then re-compress with the better Genozip compression.
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I developed a small Python script to do this:
https://github.com/MrTomRod/flower-plot
![enter image description here][1]
[1]: https:/…
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the link doesn't work. but I think it is described [here][1] by Kevin .
[1]: https://www.biostars.org/p/9473967/
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