Moderator: Jean-Karim Heriche
Jean-Karim Heriche ♦ 22k
- Reputation:
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- EMBL Heidelberg, Germany
- Website:
- http://jkh1.github.io/
- Last seen:
- 16 hours ago
- Joined:
- 8 years, 10 months ago
- Email:
- h******@embl.de
Posts by Jean-Karim Heriche
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... It depends on the type of job and type of work you want to be doing. ...
written 4 days ago by
Jean-Karim Heriche ♦ 22k
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... Even if you don't have the sequences, the GFF file should contain start and end positions so you could cluster things that overlap. Hard to tell what's possible or not without knowing what kind of data you have access to. ...
written 5 days ago by
Jean-Karim Heriche ♦ 22k
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... > So I don' t know if I could pool them under the same gene
Yes, you can. You could try clustering sequences/isoforms into "genes". ...
written 5 days ago by
Jean-Karim Heriche ♦ 22k
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... Based on what you describe, it would seem that the outcome is biased by redundancy, i.e. the same gene is represented by multiple IDs. This could be the case if you're working with transcript IDs. Try working with gene IDs instead. ...
written 5 days ago by
Jean-Karim Heriche ♦ 22k
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... Similar to doing a PhD without the degree but probably better pay would be to get a job in the domain, just look for jobs which offer some learning opportunities, for example in academic support facilities. ...
written 5 days ago by
Jean-Karim Heriche ♦ 22k
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... ChEMBL targets are primarily associated with Uniprot accessions so you'll probably need to do it in two steps. The first is to retrieve the Uniprot accession number, the second to convert Uniprot accession to Entrez gene ID.
For the first step, you have a few options:
- You can retrieve Uniprot ...
written 5 days ago by
Jean-Karim Heriche ♦ 22k
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... > Sequence names and IDs don't change
That's true only to some extent. Names used to change quite often, maybe less frequently now but can be ambiguous. IDs may be more stable but would still need a database version to be completely unambiguous. Some databases consider that a minor change does ...
written 8 days ago by
Jean-Karim Heriche ♦ 22k
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... This is the difference between reproducibility and replicability. Interested people can read the recent [National Academies report on Reproducibility and Replicability in Science][1] or for a quicker read [Reproducibility vs. Replicability: A Brief History of a Confused Terminology][2]
[1]: htt ...
written 8 days ago by
Jean-Karim Heriche ♦ 22k
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... Like blastn, other software tend to treat ambiguities as mismatches which I think is the conservative way of doing it. Also have a look at exonerate, I don't remember exactly how it treats ambiguity codes but as a last resort you could pass it a custom substitution matrix that includes ambiguity cod ...
written 8 days ago by
Jean-Karim Heriche ♦ 22k
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... Indeed. I'd be worried if a result held up only for a limited number of database versions. ...
written 8 days ago by
Jean-Karim Heriche ♦ 22k
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For A: Determination of hub genes in PPI network
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