Moderator: Michael Dondrup
Michael Dondrup ♦ 46k
- Reputation:
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- Location:
- Bergen, Norway
- Website:
- https://licebase.org/
- Last seen:
- 3 days, 5 hours ago
- Joined:
- 9 years, 4 months ago
- Email:
- m*******@gmail.com
PhD in bioinformatics. Currently Researcher at the Sea Lice Research Centre, responsible for LiceBase, an infrastructure for genomic resources of sea lice, and analysis of genomics data from emerging genomes.
Posts by Michael Dondrup
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... Hi, thanks for accepting this and I hope it helps. Given the sparsity of the information and also my lack of knowledge of the data type, I am not sure if the votes are justified yet. Please let us know how it turns out. ...
written 26 days ago by
Michael Dondrup ♦ 46k
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... Hi Friederike, first thanks a lot for the relevant hint. Maybe you would like to give an answer yourself.
For explanation, the reason for not recommending DEseq was that I was unable to find any paper that has used this combination of tools in their Methods. Whenever the terms appeared in the same ...
written 26 days ago by
Michael Dondrup ♦ 46k
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... In short, afaik, DESeq2 cannot be used for differential peak expression analysis as required by DRIP seq.
Longer answer:
That doesn't mean that one could not somehow run DESeq(2) or other DE analysis packages on these data, e.g. after re-formatting, inserting 'pseudo'-transcript regions and counts ...
written 28 days ago by
Michael Dondrup ♦ 46k
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Comment:
C: About DESeq2 analysis
... I have added a link to the DRIP seq wikipedia entry. It should be quite clear what the implications are. I have also changed the title to more specific. ...
written 28 days ago by
Michael Dondrup ♦ 46k
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... It is perfectly possible to read millions of lines in R using e.g. scan. I am guessing that the data contains SNP id's and that you want to extract a subset of rows from the larger file based on ids given in another file. I think we have multiple good solutions for this all over the place already, n ...
written 29 days ago by
Michael Dondrup ♦ 46k
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... Why call awk from python?
Anyway you have to adapt the quotes. E.g. escape them or use alternative quotes. Like qq in Perl. Don’t know if python has similar functionality
Of course it has something similar...
https://stackoverflow.com/questions/29559905/does-python-have-an-equivalent-of-perls-qq ...
written 4 weeks ago by
Michael Dondrup ♦ 46k
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... Looks like a problem for a hidden Markov model. ...
written 4 weeks ago by
Michael Dondrup ♦ 46k
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... > We are looking at the complete genome of roughly 20 000 bacterial species and we expect to find the queried gene in most of them.
That sounds like a contradiction. Please clarify
...
written 4 weeks ago by
Michael Dondrup ♦ 46k
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... You cannot use blastn for this purpose. Your nucleotide sequence is not well conserved. To find all possible orthologs you have to compare protein sequences. Use either translated protein seq with tblastn or tblastx with a nucleotide query or protein queries on a protein database from annotated prot ...
written 4 weeks ago by
Michael Dondrup ♦ 46k
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Comment:
C: low bootstrap value?
... You could also try to create alignments for each protein first, and then concatenate the alignments after that. That might avoid artificial alignments across junctions. You could also try skip the gblocks trimming step, as it also might remove some phylogenetically important regions. ...
written 4 weeks ago by
Michael Dondrup ♦ 46k
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