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Recent Replies
Comment: Post-imputation plot
by
kl
▴
10
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
•
0
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
by
ATpoint
82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot
by
LChart
3.9k
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…
Comment: RNA editing sites based on DNA seq and RNA seq
by
Adam
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30
Are those 20% unaligned reads coming after hyper-editing detection?
Answer: How to find overlap of clusters in two seurat porject
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Adam
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30
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
by
Adam
▴
30
> 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…
Answer: cnetplot category names are too long
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bkleiboeker
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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:
# my results of…
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GenoMax
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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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GenoMax
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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…
Comment: DESeq2 processing problems
by
Ram
43k
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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