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Recent Replies
Comment: Which language use as a beginner in Bioinformatics and Computational genomics
by
Mensur Dlakic
★
25k
I assume here you mean the usefulness for common tasks such as file manipulation and pipeline creations. How would one do sequence assembly…
Answer: Which language use as a beginner in Bioinformatics and Computational genomics
by
Mensur Dlakic
★
25k
There is no single language that is best suited for all areas of Bioinformatics. If one's main interest is RNA-seq, R will probably be more…
Comment: Which language use as a beginner in Bioinformatics and Computational genomics
by
Brian Bushnell
19k
It depends on specifically what you will be doing. But IMO the order of importance is Bash > Python > R.
Comment: Bam files generated with STAR cause a segmentation fault core dump error when us
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bkffadia
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![Galaxy Command Line][1]
[1]: /media/images/8c45586a-e3e3-46dd-b06b-a9788a6e
Comment: RNA seq
by
Istvan Albert
99k
there is no need to "average" anything, the point of replicates and RNA-Seq in general, is to measure the same thing several times and use …
Answer: Which language use as a beginner in Bioinformatics and Computational genomics
by
Istvan Albert
99k
I would say every scientist needs to know R - so if you don't know R it would serve you well to learn it.
In my opinion Python is not we…
Answer: using RMA normalized microarray in Limma
by
ATpoint
78k
Arrays do not have counts. RMA-proceased data are fine. See limma user guide.
Comment: RNA seq
by
ATpoint
78k
What is the question? I assume you googled 'differential RNA-seq' and tried the obvious tools such as DESeq2 and limma?
Answer: Can't install hisat2 with miniconda
by
Istvan Albert
99k
You have installed the wrong version of conda.
Even on M1 (arm64 CPU) you need to be using the Intel-based (x64 CPU) conda installer. So …
Comment: Bioinformatics: what do you think of it in the next 20 years?
by
Istvan Albert
99k
Famous poet once said:
"We are what we were - and we will become what we are."
The previous generation sets the stage for the next.
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
by
CTLong
▴
20
After reads are mapped to the genome, there are algorithms that quantify the number of mapped reads onto a genomic locus. Some of these alg…
Comment: Bioinformatics: what do you think of it in the next 20 years?
by
GenoMax
136k
> what do you think of it in the next 20 years?
It will be what people like you make of it (assuming you are just starting out and that is…
Comment: Fastest way to convert BED to GTF/GFF with gene_ids?
by
cmdcolin
★
3.4k
thanks for making these great tools
Answer: Dimensionality reduction on data sets with variable dimensions
by
Mensur Dlakic
★
25k
Not sure whether what you want to do will be informative. That aside, UMAP works with sparse data. Simply insert missing values for shorter…
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