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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
141k
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
by
BioinfGuru
★
1.7k
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…
Comment: Downloading the raw microarray data from GEO
by
GenoMax
141k
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…
Comment: Cellranger count error: Input FASTQ file ended prematurely
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GenoMax
141k
That is odd. Thanks for following-up and providing an explanation.
Answer: Cellranger count error: Input FASTQ file ended prematurely
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bp22
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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…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
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Ram
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Your tutorial required `sudo` and thus is not doable for a majority of people. Any alternative to `sudo snap`?
Comment: Should I apply doublet detection for each pool seperately?
by
Ram
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Do not delete posts that have received feedback,
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
by
_quantum_girl_
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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: …
Comment: RNA seq differential expression analysis
by
BioinfGuru
★
1.7k
https://help.galaxyproject.org/
Answer: RNA seq differential expression analysis
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The tool RSEM, which performs transcript quantification for RNA-Seq data, provides FPKM.
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Enrique
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Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
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The information do not suffice. Please show plots and identified marker genes. Also, make sure it is not a trash cluster with low number of…
Comment: Free/open source 23andme-like analysis
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joe
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Thank you, I added 'accurate' now ;)
I'm surprised to find out that there isn't some tool like multiqc that just summarizes all this infor…
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Guys, just use `samtools sort` which won't get you into trouble with any of that.
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