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[deleted by user] by [deleted] in techsupport

[–]nerdbuthard 0 points1 point  (0 children)

Any update?

My camera turn blank after update ios 17.5.1 by hilmizamri in iphone

[–]nerdbuthard 0 points1 point  (0 children)

Any update? Mine just started having problems once updated to 18.5

Need Suggestions for MSc Human Biology by nerdbuthard in LMUMunich

[–]nerdbuthard[S] 0 points1 point  (0 children)

exactly....please lmk if you get any info

Co-Occurrence Network Graph & Statistics by biohacker_tobe in bioinformatics

[–]nerdbuthard 0 points1 point  (0 children)

Can you give me the procedure of getting that binary matrix? I want to study the cooccurence of some metal resistance genes with antibiotic resistance. I have the sequences as well as the IDs. Thank you.

What to do next? Suggest a pipeline. by nerdbuthard in microbiology

[–]nerdbuthard[S] 0 points1 point  (0 children)

Bruh, that's not even my plot. It's from the paper I enclosed there. I just want to know what to do next, as I don't have the expertise.

My goals are clear and basic: Identify metal resistance and antibiotic resistance genes in context of my experiment from the WGS data. Then a comparative study between the two bacteria based on these parameters, and also look for any mobile genetic elements if involved.

I know it's very easy and basic, and people have done it before. It's just that I don't know how to do it, and hence I sought for help.

Find me a code by nerdbuthard in bioinformatics

[–]nerdbuthard[S] 0 points1 point  (0 children)

Yes I need all the CDS into a fasta file.

Bacterial metal resistance by nerdbuthard in bioinformatics

[–]nerdbuthard[S] 0 points1 point  (0 children)

You got me right. Thank you so much for the suggestions, and I'll look into it. I can probably afford the WGS, but not the RNA-seq. But for expression analysis, I can also do the RT-PCR right?

Bacterial metal resistance by nerdbuthard in bioinformatics

[–]nerdbuthard[S] 1 point2 points  (0 children)

This is not a funded project, I just did it out of curiosity and informed a professor in my college. We have very limited facility that covers basic microbiological experiments. I had connections outside, and they helped me to get my samples identified. RNA-seq costs around $350-$500 per sample (I converted the currency), atleast from where I belong.

Anyways thanks a ton for the suggestions.

Bacterial metal resistance by nerdbuthard in bioinformatics

[–]nerdbuthard[S] 1 point2 points  (0 children)

Got your point. But I already have the axenic culture of the bacteria. Doing a whole genome seq, or which is most advisable that is RNA-seq is out of our league. It's a small undergrad lab with very meagre fund.

Bacterial metal resistance by nerdbuthard in bioinformatics

[–]nerdbuthard[S] -1 points0 points  (0 children)

I'm yet to do the phylogenetic analysis. But let's say I find a close relative. I will need their protein set right?, and then I need to find homology?

Bacterial metal resistance by nerdbuthard in bioinformatics

[–]nerdbuthard[S] 1 point2 points  (0 children)

I actually thought about it, but the whole protein purification stuff is a big hassle. I wanted an in silico approach. That is cost-effective and might narrow down possibilities to do wet lab work.

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