User: predeus

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predeus1.5k
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Principal bioinformatician at Wellcome Sanger Institute. Former research director of Bioinformatics Institute (Saint Petersburg). 

Posts by predeus

<prev • 191 results • page 1 of 20 • next >
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Answer: A: RNA-seq ribosomal genes vs proteins
... I think they QC different things - and don't necessarily correlate. Ribosomal RNA shows how much of it is captured from this particular sample - since rRNA is 99% of all cell's RNA anyway, you won't really see any changes due to cellular state, I think. Ribosomal proteins, on the other hand, change ...
written 1 day ago by predeus1.5k
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Comment: C: Cell type assignment for non-model organism single cell RNA-seq
... I've seen it used in human or mouse datasets, yes. But it's really a completely different world when you go into non-mammalian cells.. ...
written 8 days ago by predeus1.5k
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Comment: C: Cell type assignment for non-model organism single cell RNA-seq
... Yes - often there is no such thing as a closely related organism, since the space of scRNAseq-sequenced animals is very sparse :) but still, there must be few hundred done, and having no automated tool is quite strange. ...
written 8 days ago by predeus1.5k
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Cell type assignment for non-model organism single cell RNA-seq
... Hello all, It became very popular for "genomic zoologist" researchers to do single cell RNA-seq of the whole animal in order to study the available cell types. However, in almost any paper the cell type assignments are done using very few markers and by painstaking manual classification. Do you ...
scrna-seq non-model organism rna-seq single cell written 10 days ago by predeus1.5k
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Answer: A: Suggest common programming tasks for biologists who are novice programmers
... The most useful skill is text parsing, summarisation, and re-formatting. Knowing how to convert one text-readable format into another or summarise/extract values from text file is very, very useful. ...
written 11 days ago by predeus1.5k
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Comment: C: Best Practices for chi-seq analysis
... Take a look at [what ENCODE did](https://www.encodeproject.org/data-standards/chip-seq/) for a more complete pipelines. ...
written 17 days ago by predeus1.5k
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Answer: A: Searching for human genotyping data thats not public
... That's a very strange request. You really need to clarify it with him - as in, what is the idea behind this. The best place for human allele frequencies is [gnomAD](https://gnomad.broadinstitute.org/); however, these variants can hardly be viewed as novel. By far not all of them are characterised, ...
written 17 days ago by predeus1.5k
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Answer: A: Best Practices for chi-seq analysis
... There are two big classes of problems - narrow peak and broad peak Chip-seq. For narrow peaks, classic analysis with alignment by any good genome-wide aligner (e.g. `bowtie2`) and peak calling by `MACS2` should work well. Downstream analysis tends to be focused on motifs, which can mostly (in firs ...
written 18 days ago by predeus1.5k
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Answer: A: Algorithm to remove batch effects
... [This](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1850-9) is a very useful paper. There's also github for the comparisons they've ran. ...
written 21 days ago by predeus1.5k
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Answer: A: Which aligner for human WGS
... I agree with the answer @ATpoint gave - `bwa mem` is an old and well-established tool for this task. However, if you want to be very up-to-date, [Isaac4](https://github.com/Illumina/Isaac4) has shown the highest performance in latest benchmarks. It would probably be faster too. ...
written 21 days ago by predeus1.5k

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