User: f.a.galkin

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f.a.galkin40
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Germany
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1 year, 1 month ago
Joined:
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Posts by f.a.galkin

<prev • 17 results • page 1 of 2 • next >
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Comment: C: UK sequencing services
... Oh, I am sorry for breaking the rules But thank you for posting the links: they seem to be just the thing I was looking for ...
written 13 months ago by f.a.galkin40
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(Closed) UK sequencing services
... Hello, I would like to order stool sample WGS sequencing in UK, but I have no idea, what companies provide such services there. Could you direct me towards commercial sequencing laboratories? More specifically, I want to receive Illumina HiSeq 2000 reads of 5 samples. The samples should be analyze ...
wgs uk sequencing commercial illumina written 13 months ago by f.a.galkin40
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Answer: A: Tools For Metagenomic Data Analysis
... I really liked using [Centrifuge][1] for WGS taxonomic profiling. It is resource efficient (has a 6GB index for all bacteria, compared to Kraken's over 100GB) and produces an abundance table when it's finished. [1]: https://ccb.jhu.edu/software/centrifuge/manual.shtml ...
written 16 months ago by f.a.galkin40
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Comment: C: Tools For Metagenomic Data Analysis
... Is FANTOM alive? Their download and manual links aren't working for me ...
written 16 months ago by f.a.galkin40
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Answer: A: metagenomic analysis pipelines for gene prediction, annotation and functional an
... I am also looking for functional profiling software atm and I have come across MOCAT2 and NGLess But these seem rather heavy weight, as they require an assembly stage. I wonder if there are any light weight options for functional analysis. Maybe just blasting each read would be more sensible. If y ...
written 16 months ago by f.a.galkin40
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Comment: C: Metagenomics community profiling approaches.
... It does contain, but I am looking for alternatives, if there are any. Centrifuge's report assigns zero abundances too generously ...
written 16 months ago by f.a.galkin40
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Comment: C: Metagenomics community profiling approaches.
... Marker gene based method are biased and do not guarrantee detecting all the present organisms ...
written 16 months ago by f.a.galkin40
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Comment: C: Metagenomics community profiling approaches.
... K-mer based, Centrifuge, mapped onto their index of bacterial/archaeal genomes ...
written 16 months ago by f.a.galkin40
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Metagenomics community profiling approaches.
... After I map a metagenome against a DB, I don't get an abundance table per se. I need to somehow decide, how I treat non-unique mappings and normalise data. [Centrifuge][1] suggests an EM-based method, but what are the alternatives? I can try basic RPKM that completely ignores the problem, or I can ...
wgs metagenomics community binning written 16 months ago by f.a.galkin40
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Comment: C: Metagenomics: rationale behind Q trimming
... That makes sense I guess, I'll just set Q=4 to make sure nts are more likely to be right than wrong. I guess there's no way of finding out if it works other than testing it ...
written 16 months ago by f.a.galkin40

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