User: robert.murphy

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Posts by robert.murphy

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Are there methods to identify a bacteria as anaerobic or aerobic through its whole genome?
... I have several bacterial genomes that I know from literature are either anaerobic or aerobic but I was wondering if there are computational methods or tools to identify this also? ...
genome written 13 days ago by robert.murphy10
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Comment: C: Is there a tool for creating publication quallity phylogenetic tree with metadat
... Do you just mean node labels? ...
written 23 days ago by robert.murphy10
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Comment: C: Is there a tool for creating publication quallity phylogenetic tree with metadat
... What would I then do with the character representation of the number? ...
written 23 days ago by robert.murphy10
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Comment: C: Is there a tool for creating publication quallity phylogenetic tree with metadat
... Unfortunately iTOL does not allow you to annotate with numerical values I believe ...
written 23 days ago by robert.murphy10
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Is there a tool for creating publication quallity phylogenetic tree with metadata associated with each leaf
... I have generated a collapsed phylogenetic tree of 122 orthologs across 34 samples and now want to present the tree with metadata about the original genome such as sequence quality metrics, short of putting a table next to it in PowerPoint is there a tool that would allow me to attach such metadata t ...
alignment written 23 days ago by robert.murphy10 • updated 23 days ago by antonioggsousa920
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Comment: C: Comparing two sets of 16s sequences to identify any identicle (within 97%) seque
... I am looking between files :) I will give CD-HIT a look. ...
written 3 months ago by robert.murphy10
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Comparing two sets of 16s sequences to identify any identicle (within 97%) sequences
... I have two sets of 16s sequences and want to see if there are any sequences within 97% similarity. Blastn uses local alignment and I am looking for global alignment (I think? please correct me on this). If I am indeed looking for global alignment what is an appropriate took to use that will return a ...
genome alignment written 3 months ago by robert.murphy10 • updated 3 months ago by Mensur Dlakic6.0k
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Comment: C: BUSCO vs CheckM, which is best for determining bacterial genome completness.
... Thank you this advice, it is helpful :) ...
written 3 months ago by robert.murphy10
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BUSCO vs CheckM, which is best for determining bacterial genome completness.
... I have 21 bacterial isolates from termite guts and I want to determine the completness of the genomes. Which tool between BUSCO and CheckM is best to do this? ...
genome written 3 months ago by robert.murphy10 • updated 3 months ago by Mensur Dlakic6.0k
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Comment: C: Scanpy vs DeSeq for single cell RNASeq DE gene analysis
... These links are very useful but are all about analysis, I think my misunderstanding is in the differences between bulk RNAseq and scRNAseq. I have previously looked but been unable to find a recourse to inform me on this. However it also appears the main differences are actually in the analysis. but ...
written 5 months ago by robert.murphy10

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