Moderator: jrj.healey
jrj.healey ♦ 9.1k
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Recently finished my PhD, so now I pretend to know what I’m talking about on Bioinformatics forums...
Posts by jrj.healey
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C: How to judge MSA from tree?
... Deciding which alignments are best is still quite subjective. You might be most interested in an alignment which preserves an active site best or something which is relevant to the overall question.
It’s not uncommon for people to edit an alignment manually by eye though because humans are still qu ...
written 1 day ago by
jrj.healey ♦ 9.1k
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C: How to judge MSA from tree?
... There are lots of additional factors you haven’t mentioned. What kinds of sequences are they? (Protein or DNA).
The algorithms are not necessarily equivalent. A neighbour joining tree and a maximum likelihood tree will very often find different topologies for example, even if the starting alignment ...
written 1 day ago by
jrj.healey ♦ 9.1k
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... As finswimmer mentioned, the minimum we need is an example of your input so we know what manipulations are needed to create your desired output. ...
written 1 day ago by
jrj.healey ♦ 9.1k
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... That’s usually only true if the depth of coverage is astronomically high, and even then it’s not guaranteed to cause issues. It usually matters a lot less for smaller sequence like phage. I would assemble all your reads first and see what you get before you start arbitrarily breaking them up. ...
written 3 days ago by
jrj.healey ♦ 9.1k
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... Why would you separate the reads out like that? The assembler will intrinsically give you back the best “consensus” contigs, thats it’s job. ...
written 3 days ago by
jrj.healey ♦ 9.1k
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... +1 for using gains as an example! ...
written 4 days ago by
jrj.healey ♦ 9.1k
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... That could certainly help I would expect ...
written 5 days ago by
jrj.healey ♦ 9.1k
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... Feel free to post more questions sure. I wouldn’t say that I’m particularly an expert in this specific area, but happy to help if I can. Just make sure any questions you ask are well defined and answerable in a specific manner ideally. ...
written 5 days ago by
jrj.healey ♦ 9.1k
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... BioPython is designed to be 'glue'. To help convert file formats, provide an easy to use, unified front end for many common bioinformatics tasks. At its core it's just a clever way of storing/representing sequence data. It isn't designed to do heavy lifting like read mapping.
Even for alignments fo ...
written 5 days ago by
jrj.healey ♦ 9.1k
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C: How to align reads on reference?
... Why not use subprocess? This is exactly what it's for. Though it adds a layer of complexity over just using a shell script.
You wouldn't want to write an aligner in python anyway, it would be painfully slow and inefficient, though like any good programming language, you can *in principle* code the ...
written 5 days ago by
jrj.healey ♦ 9.1k
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