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Recent Replies
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
Matthias Zepper
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It is not entirely off, but evidently also not correct.
Melanin biosynthesis is a multistep process, that indeed prominently involves the…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
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Ram
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> so a single Rscript could utilise multiple environments and versions
How is that sane, let alone "better"? Also, why use `snap` for curl…
Comment: how to find genes that are significantly expressed in brain cortex samples
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Ram
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Normalized how?
Comment: Duplicate marking, read names, and the SRA
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GenoMax
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With public data one has to work with what is there. If the information about position is absent then only thing that could be done is to l…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
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BioinfGuru
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Or better yet. To have an R package that allows access to conda environments via "conda list env" so that environments can be switched with…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
GenoMax
141k
If GPT is right then it says that:
> The specific gene responsible for the orange and non-orange (black or
> gray) fur colors in cats is t…
Comment: what's the genomic location and name of gene responsible for orange and black pa
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Jean-Karim Heriche
27k
As far as I know the Orange locus hasn't been mapped to a gene. Maybe this paper will help in narrowing the search: https://www.ncbi.nlm.ni…
Comment: Duplicate marking, read names, and the SRA
by
Luka
•
0
>Curios if there a reference for this?
[Apparently it's not deprecated yet][1], but will be soon and the SRA intends for it to be at some …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
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Ram
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I prefer RStudio for new projects as well. The moment I need versions though, RStudio becomes a burden. I wish one could launch RStudio fro…
Comment: what's the genomic location and name of gene responsible for orange and black pa
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GenoMax
141k
According to ChatGPT: The gene responsible for the orange and black patches of fur in calico cats (and tortoiseshell cats) is the X-linked …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
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BioinfGuru
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Certainly true. Switching versions is way simpler that way, at the cost of the familiarity of the Rstudio IDE - especially if the code is w…
Comment: Duplicate marking, read names, and the SRA
by
GenoMax
141k
> fastq-dump is deprecated
Curios if there a reference for this? `fasterq-dump` seems to allow for parallel streams but `fastq-dump` is st…
Comment: Duplicate marking, read names, and the SRA
by
Luka
•
0
>In many cases those remain recoverable using the -F option when you dump the data (cloud download not required)
The -F option (or any equ…
Answer: Duplicate marking, read names, and the SRA
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GenoMax
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To be specific, not every dataset in SRA loses the original identifiers. In many cases those remain recoverable using the `-F` option when …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
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Ram
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To use different versions of R and bioconductor, you don't really need RStudio. One can simply create new conda environments with the requi…
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