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Recent Replies
Answer: Bacterial plasmid analysis
by
Mensur Dlakic
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If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
Comment: POSSUM not working due to incompatible pssm file
by
rianna.collins
•
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Thank you so much. I'm new to this and didn't realise there was a code option.
Answer: Is there a way to increase the automatic label text size in Cytoscape?
by
Scooter
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Greetings,
Are you saying that you can't use the size setting in the style tab? That should certainly work, as should the label size se…
Answer: Basic stats in hierfstat
by
mdav
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Hi Zoe, did you find an answer for this? I am also getting the same error.
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GenoMax
141k
Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
Comment: Post-imputation plot
by
kl
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Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
•
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I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems
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ATpoint
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Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
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LChart
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I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
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Adam
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Are those 20% unaligned reads coming after hyper-editing detection?
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I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
Answer: DESeq2 processing problems
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Adam
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> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
•
0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
> however I'm not sure this would be appropriate in my case as the plasmid sequences are obviously much more diverse and vary in size
Can…
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