User: edward.messick

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Posts by edward.messick

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Comment: C: what is the motivation of a person for being a cancer research bioinformatician?
... your ability to do something now and your intrinsic motivation/passion/desire do not need to be completely related. like you said, every job requiring such advanced knowledge/skills will have a learning curve. I think most cancer centers are looking for people who want to work on cancer for one re ...
written 8 weeks ago by edward.messick40
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Comment: C: Does anyone know good open data sources for metagenomic data linked to a given
... thanks! I'll look through that post... of course I'm probably being a little too nitpicky with my search... we'll never really find ideal data in the real world, will we? ...
written 9 weeks ago by edward.messick40
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Does anyone know good open data sources for metagenomic data linked to a given condition?
... I'm looking for either a database (like SRA) or even a study that provides its data that has labels associated with the data. Ideally, this would be metagenomic data (either sequences or abundance tables) in a study that has a strong link between a feature like a species and the condition being stud ...
open data metagenomics databases written 10 weeks ago by edward.messick40 • updated 9 weeks ago by erictleung90
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Comment: C: What are those "ENOG" numbers in eggNOG 4.5?
... awesome! thanks a lot - exactly what I need ...
written 5 months ago by edward.messick40
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Answer: A: What are those "ENOG" numbers in eggNOG 4.5?
... extending this question, is there any database/flat file that has functional categories and/or associated gene/protein to each ENOG value? this exists for COGs but now that you have pointed out that COG's change between versions of eggNOG, I am no longer sure that these flat files are even usable.. ...
written 5 months ago by edward.messick40
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Comment: C: Comparison of 16S- & WGS-derived community composition
... Sorry about the (very) delayed reply. After further study, 16S seems to be better for certain use-cases but I'd almost always suggest WGS at this point. There is also the major advantage of WGS being able to identify non-bacterial microbes, while 16S is limited to bacteria. Shoot me an email if y ...
written 6 months ago by edward.messick40
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Answer: A: Comparison of 16S- & WGS-derived community composition
... I've run across a few studies that touch on this topic, I'll have to compile them and come back to this. But I've studied this myself for a while and WGS seems to be better for everything now, if implemented correctly. It hits species level specificity, whereas 16S is only sensitive at the genus l ...
written 10 months ago by edward.messick40

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