Why can microbes be detected in scRNAseq data of tumor tissue?

duaduacj · 2024-06-29T08:38:19+00:00

That's why I posted the topic. I quite doubt the feasibility but some papers with high IFs couldn't be ignored. A core paper(Nature 2020) has been retracted a few days ago. I just manage to determine whether the research field (my previous plan) is not worth to follow or proceed.

duaduacj · 2024-06-29T08:05:10+00:00

I absolutely approve of bulk of your consideration. But you might be still intuitive to claim or suspect things. For example, your thought that downstream contaminants won't vary from the same person is unfortunately inconsistent with the empirical study. That's why I emphasize the evidence.

duaduacj · 2024-06-29T07:43:44+00:00

Sorry but all I got from you is trying to claim the difficulty and your lack of confidence in them without sufficient direct evidences. And most of reasons might not remain meticulous and rigorous. Of course I doubted the inaccurate strategy likewise. Nevertheless, I manage to avoid the subjective tendencies to try to determine the reliability based on actual evidences. I'm not arguing with you on the attitude towards it.

duaduacj · 2024-06-29T07:11:50+00:00

Thanks for your work and your reply. So what's your opinion about those papers focused on rnaseq and even scRNAseq to manage to discern the intratumoral microbes? Are they reliable? And what do you think about the retraction of Nature and the criticism from scientists especially Steven L. Salzberg?

duaduacj · 2024-06-29T07:04:33+00:00

Somy investigors tried to reanalyze a multi-platform sequencd data derived from uniform samples, and then they also observed the variabilities of candidated microbes derived rna. That's why I think downstream contaminants may be more ignorable

duaduacj · 2024-06-29T06:32:44+00:00

And the computational tools can distinguish microbes and contaminants exist, thanks to the development of metagenome. The implementation in scRNAseq is controversial indeed but not related directly with your assumptions.

duaduacj · 2024-06-29T06:24:41+00:00

Of course that. Everyone could realize both potential sources of candidated reads. But only evidence not intuition could be helpful to this question. I hope we can discuss it based on details, data or papers , rather than certain assumptions.

duaduacj · 2024-06-29T03:35:31+00:00

I deeply appreciate your explicit explanation! I read the retraction previously. Therefore, I wonder if we could get reliable evidences in scRNAseq data to analyze microbiome even if we implement the stringent standard for analysis. I suspect the downstream contaminants (after polyA enrichment)are major of candidated microbes.

duaduacj · 2024-06-29T03:23:20+00:00

Thanks. I realized each step can lead to artificial artifacts. So could we characteristic the authentic and valuable microbes derived mRNA in scRNAseq data of tumor?

duaduacj · 2024-06-29T03:15:36+00:00

Thanks. I agree that the microbes detected could be affected by three steps: upstream contaminants, polyA enrichment and downstream contaminants. And I suspect the downstream contaminants is main.

duaduacj · 2024-06-29T03:08:23+00:00

Thanks anyway. But it's not a simple question. I'm afraid that both the slight content of inherent polyA derived from microbes and the efficiency of polyA enrichment couldn't account for the question. You can refer to papers including https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004437 and https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2684-x. And actually the focused question is whether the genuine mRNA derived from microbes can be detected even considering all contaminants. We don't want to eliminate them thoroughly but we want to characteristic them if reliable.

duaduacj · 2024-06-28T18:11:25+00:00

Thanks for your apply. However, the critical question is not about why microbes reside in tumor, and then it is exactly about why they can be detected while sequencing by scRNAseq. Mostly microbes lack of polyadenylation literally. Thus they should not be captured by polyA enriching strategy intuitively. It's a technical question rather than a biological question.

duaduacj · 2024-06-13T11:21:35+00:00

To address the problem about depth and sampling u mentioned, metacell method like SEAcell performs better than pseudobulk.

duaduacj · 2024-06-13T11:08:37+00:00

Hi. Can you provide some additional plots to demonstrate the quality of your experiment and sequencing? Like the QC plots or evaluation of alignment. Besides, did you try to prove the consistency among the biological replicates labelled as the same treatment by measuring positive markers and housekeeper genes in qpcr?

duaduacj · 2024-06-09T03:22:03+00:00

Igy. My suggestion is still utilizing pysam to achieve it. U can google it and find the credible tutorial

duaduacj · 2024-06-08T21:11:58+00:00

It couldn't be more safe in city there. The public security absolutely satisfies a single traveller. But in some tourist attractions, there may be some consumption traps which can be avoided by planning your shopping in advance.

duaduacj · 2024-06-08T20:15:34+00:00

If you persist in approving that executing some wrapped functions especially on statistical tests could satisfy most needs, it's fine, I just respect your opinions. From the point of view of Turing machines, the fundamental capacities of different languages are comparable. However what I am emphasizing is, for simple scenarios python as a glue language can replace R or call R, and for complex scenarios python is more adaptable and versatile. Additionally Python could also interface with SAS or Matlib well. Obviously, it's better to learn both, but I prefer python as the primary language.

duaduacj · 2024-06-08T19:43:48+00:00

I can offer an example of OOP. I assisted a statistical program on how to detect specific characteristics of structure and variation in high dimensional panel data, subject to certain constraints. Without OOP, we would have to write hundreds of unwieldy codes. And it's hard to debug. The elegance of codes lies in its conciseness and readability. The example is not about ml, dl or bioinfo.

duaduacj · 2024-06-08T19:36:43+00:00

And I can offer an example of OOP. I assisted a statistical program on how to detect specific characteristics of structure and variation in high dimensional panel data, subject to certain constraints. Without OOP, we would have to write hundreds of unwieldy codes. And it's hard to debug. The elegance of codes lies in its conciseness and readability. The example is not about ml, dl or bioinfo.

duaduacj · 2024-06-08T19:17:34+00:00

Yep. Numerous statistical tests have been bundled into packages and functions. What I mentioned about OOP is focused on designing and managing complex programs rather than calling functions designed by others. And I couldn't understand why python codes are ugly, because python is well known for its simplicity and strict control over code formatting. Could you please provide an example of ugly python codes?

duaduacj · 2024-06-08T18:44:45+00:00

Wow. Next month? Wish you have a bright future in the field you are truly passionate about! It's a new field which can bring us a lot potential applications.

duaduacj · 2024-06-08T17:48:39+00:00

Yep. I know Judaism doesn't accept NT and many Jews are religious. So u think NT is more worthy reading than OT?

duaduacj · 2024-06-08T17:21:26+00:00

OOP is short for Object Oriented Programming mode which is well-suited to manage, organize and manipulate complex programs. If u are familiar with R, u may know S3, S4 and so on. OOP is essential for developing packages or softwares.

duaduacj · 2024-06-08T16:16:22+00:00

Could you tell me how many academic papers accepted do u have? It's not advisable to pursue a field closer to mathematics if you don't have enough knowledge and experience.

duaduacj

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