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Comment: Duplicate marking, read names, and the SRA
by
GenoMax
141k
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
by
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…
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GenoMax
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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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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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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
by
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
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> 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
by
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
by
Ram
43k
To use different versions of R and bioconductor, you don't really need RStudio. One can simply create new conda environments with the requi…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★
1.7k
Done. Thank you.
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
by
GenoMax
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Perhaps add the word linux/ubuntu to the title? You have noted that the instructions are for Ubuntu in text.
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
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BioinfGuru
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Thanks @Ram I'll add that to the intro. I'm the admin on my machine so I haven't found it necessary to install any other way. I'll try a fr…
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