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Recent Replies
Answer: bwa-mem keeps failing to locate the index files
by
SIMONE
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in my code the reference is .fasta, not .fa, i don't this could be the issue
Comment: prokka with too many "hypothetical proteins" and genome comparison
by
avinci1
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I'm working with everything I have, to be honest. I will work with aa sequences and try MMseq2.
Thank you so much for the help!
Comment: Analysing Microarray Data In Bioconductor
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Hi! Did you find it? I am struggling with gene expression meta-analysis, but don't know how to strat the analysis. Do you have any material…
Comment: prokka with too many "hypothetical proteins" and genome comparison
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Dunois
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Are you working with nucleotide sequences or amino acid sequences? It's best to perform all these kinds of sequence comparisons with the la…
Comment: prokka with too many "hypothetical proteins" and genome comparison
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Thank you so much for your help.
I don't know how usual is to have 50% of hypotetical proteins. If I have to give you a number they are aro…
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it is very unlikely that the number of mutations caused the reads to fail to align. The number of mutations needed to cause that would be v…
Comment: prokka with too many "hypothetical proteins" and genome comparison
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What is the organism? 50% hypothetical isn't that crazy to me if its something a bit unusual. I spent my PhD working on a gene cluster wher…
Comment: prokka with too many "hypothetical proteins" and genome comparison
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We tried to select the specific database for the bacteria, but the result was the same. All hypotetical proteins. At least half of the outp…
Comment: prokka with too many "hypothetical proteins" and genome comparison
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What do you mean there are too many? It is normal to encounter a lot of hypotheticals unless its a very well characterised organism.
If it…
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I would test the celltype and treatment effect here via the averages, for example for the celltype effect as below. I think that's one way …
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Basically I sent the DNA of both bacteria to a sequencing service and they gave us the annotation files, with excel files, prokka annotatio…
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What state are these genomes in? Single contig or multiple pieces. Were they assembled from short or long read data? Where did these bacte…
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If I use Celltype_Condition as a contrast, there would be four levels : CelltypeA_Control, CelltypeA_Treated, CelltypeB_Control, CelltypeB_…
Comment: prokka with too many "hypothetical proteins" and genome comparison
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I have two bacteria genomes that I isolated and I have to know if they are the same or not, and if not, how much they are different.
The pr…
Comment: prokka with too many "hypothetical proteins" and genome comparison
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what exactly do you need to compare? on the gene/protein function level or just compare absence/present of genes ?
You can (crude approach…
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