Moderator: WouterDeCoster
WouterDeCoster ♦ 32k
- Reputation:
- 31,780
- Status:
- Trusted
- Location:
- Belgium
- Website:
- https://gigabaseorgiga...
- Twitter:
- wouter_decoster
- Last seen:
- 4 hours ago
- Joined:
- 2 years, 6 months ago
- Email:
- d*************@gmail.com
I'm a PhD student at the University of Antwerp (VIB Center for Molecular Neurology) with a background in biochemistry. I mainly work on data generated by genome sequencing, exome sequencing, targeted resequencing, RNA-seq and Nanopore Sequencing using MinION and PromethION.
Posts by WouterDeCoster
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... PAA* because they make it harder to read your post. In this case, it's probably "variant calling" what you are talking about. While VC may be a CUA** for you, this is not not necessarily the case for the rest of the users here.
\* Please Avoid Abbreviations
** Commonly Used Abbreviation ...
written 4 hours ago by
WouterDeCoster ♦ 32k
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Comment:
C: snpEff: wrong HGVS output?
... Hi Marvin,
There is no need to delete your question, especially when people have provided helpful reactions.
Cheers,
Wouter
...
written 4 hours ago by
WouterDeCoster ♦ 32k
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C: Read Name in IGV and duplicates
... https://www.biostars.org/p/309884/ ...
written 22 hours ago by
WouterDeCoster ♦ 32k
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Comment:
C: Orthomcl clusters to fasta
... There is no need to SHOUT. I have removed the uppercase characters from your title. ...
written 22 hours ago by
WouterDeCoster ♦ 32k
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... Essentially, you want to filter out lines in which the number of alternative alleles is higher in the child than the sum of the alternative alleles in the parents.
But I'd say that a scenario where you have 1/0 and 0/0 parents and a 1/1 child is extremely unlikely. Also, you are probably looking fo ...
written 22 hours ago by
WouterDeCoster ♦ 32k
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... > To my knowledge, de novo variants cannot be phased by the tool because they are not transmitted from the parents.
True, but you could just filter for variants which are found in the child and not in the parents. Phasing might work to filter a bit, but why would you?
> Because there is alm ...
written 1 day ago by
WouterDeCoster ♦ 32k
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... I have moved the comment of cpad0112 to an answer so it can be accepted. ...
written 1 day ago by
WouterDeCoster ♦ 32k
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... We have sequenced NA19240, the data is available on ENA, and accession identifiers can be found in this blog post: https://gigabaseorgigabyte.wordpress.com/2018/05/24/promethion-human-genome-na19240/ ...
written 1 day ago by
WouterDeCoster ♦ 32k
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... It wouldn't be too hard to write a script which converts between one and three letter codes. There must be ample python examples to get you started. ...
written 2 days ago by
WouterDeCoster ♦ 32k
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Comment:
C: Metagenomics - mothur
... I don't know how you are trying to open the file now, and I don't know your operating system. But if you are on a linux system you can open the image using `eog`.
eog myimage.svg ...
written 2 days ago by
WouterDeCoster ♦ 32k
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For A: Merge vcf files of structural variants
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