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Recent Replies
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★
1.7k
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
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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
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>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…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
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BioinfGuru
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Done. Thank you.
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
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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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No GPR files with this data unless you ask the submitters for them directly. You can find the matrix of data here: https://ftp.ncbi.nlm.nih…
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That is odd. Thanks for following-up and providing an explanation.
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Dear all,
The reason for the error was due to the index (I1) fastq files, for example `SI-GA-A1_1_S1_L001_I1_001.fastq.gz` having a lo…
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Your tutorial required `sudo` and thus is not doable for a majority of people. Any alternative to `sudo snap`?
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Do not delete posts that have received feedback,
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They aren't merging any datasets. Just for reference the paper is this: https://www.nature.com/articles/s41380-022-01674-9#MOESM1. Citing: …
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