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Recent Replies
Comment: Bacterial plasmid analysis
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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…
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Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
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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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Adam
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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
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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…
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> 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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I'm sure someone could find a more elegant solution using `stringr::str_wrap`, but for a one-time solution I did this:
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You could edit the SAM file but I wonder if this problem is present in your original fastq data file so if not inconvenient do the alignmen…
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> I keep getting error.
Without providing information about the actual error no one can help. Please edit the post and add this informati…
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This is an open science community, not a place to write an email to Michael Love. Please address the entire community.
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kl
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All of them are G/C and A/T variants
Some seem mismatches based on AF and some seem to need flipping. I guess I am confused, as in the Mich…
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