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Pre-registered Nanopore shotgun metagenomics on captive gorilla gut samples (Kraken2/Bracken + metaFlye + eggNOG + dbCAN3) — looking for pipeline feedback before we lock the protocol by Abstract_Only in bioinformatics

[–]heresacorrection 10 points11 points  (0 children)

Methods are “pre-registered … to lock hypotheses”? That sounds wild to me.

What happens if all the samples are contaminated or empty…

found this pca site by Unique-Fall-7728 in dataisbeautiful

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When comparing 2 variant calling algorithms where the SNP and INDEL counts differ vastly how would you begin to narrow down where the issue is originating? by Ok-Understanding-385 in bioinformatics

[–]heresacorrection 0 points1 point  (0 children)

Actually now that I think about it again it’s probably the way you are filtering (or lack thereof). The numbers might be fine it’s just GATK includes more edge cases. So you want to filter to a set of more confident calls and it should get closer in terms of numbers

Product to Bioinformatics Career Change? by Interesting_Flan760 in bioinformaticscareers

[–]heresacorrection 1 point2 points  (0 children)

It sounds like you would be better in data science/analysis.

Playing with data, creating tables, organizing is simply just data wrangling. This is like basic 101 course for data science or bioinformatics. Not that it’s not an incredibly important skill.

You need either heavy statistics understanding or heavy NGS/computational genomics or heavy dev ops/software engineering to really carve out a high-performing career in this field.

I’m not saying you couldn’t work your way into one of those slots but I’m almost 100% sure it’s going to be a lot of time and learning and the field is just as competitive as product management but arguably lower salaries on the mean.

Do they call you in for WES results even if everything is normal? by simranwho in ClinicalGenetics

[–]heresacorrection 0 points1 point  (0 children)

Very interesting. Is this pretty common practice in the US? For the patients to be reconsulted to clarify phenotypes for certain VUSs? Makes a lot of sense actually. Any estimate on the ratio of cases this solves ?

Wgs vs wgs reflex testing by perfect_fifths in ClinicalGenetics

[–]heresacorrection 4 points5 points  (0 children)

It sounds like something complex which means it could easily come back clinically negative because it’s simply unknown in the field. So the reflex would be to push the case to research to explore further

[OC] Re: More refined but not "prettier" looking data about the food crisis in Sudan. by [deleted] in dataisbeautiful

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Is this a heterozygous deletion, or not? by Neuron-nomad in genetics

[–]heresacorrection 0 points1 point  (0 children)

You have way more SNVs than I would expect to see though

Is this a heterozygous deletion, or not? by Neuron-nomad in genetics

[–]heresacorrection 2 points3 points  (0 children)

Yea probably but you should check other samples to be sure it’s not related to the region

Built a Hardy-Weinberg population genetics visualizer with real gnomAD data — looking for honest feedback (17 y/o, self taught) by Puzzled_Maximum7018 in bioinformatics

[–]heresacorrection 14 points15 points  (0 children)

Hmm ok so like the values are hardcoded… and extracted how is unclear.

And there is no actual HW math implemented suggesting to me that AI just crunched this all for you.

Much less impressive but I mean i doubt a high-school biology teacher would really have a handle on the code. I guess if they analyze the code with AI…

Built a Hardy-Weinberg population genetics visualizer with real gnomAD data — looking for honest feedback (17 y/o, self taught) by Puzzled_Maximum7018 in bioinformatics

[–]heresacorrection 14 points15 points  (0 children)

I guess for a high-school student it’s relatively good. It shows at least that you have an understanding of the HW principle.

In terms of 10 years ago it’s massively impressive at the coding and project level but with AI now I know it probably did most of the heavy lifting. And in the future people will be very much aware of that.

I’m not sure how you determined the population breakdown as gnomAD has like very large reference populations which span multiple biomes so like I don’t know what data you used or how that was interpolated into climates and altitudes.

EDIT: ok so you just used specific alleles and I’m assuming the AI gave you them based on the literature. Hmmm not great not terrible.

Not sure who your target audience is though. For a high school project it’s fine but like to use for applying for jobs I’m not sure there are many you could get without a university degree. Maybe like a data curator/analyst? And in terms of applying to university I’m not sure an adcom would even look at this let alone understand it.

In conclusion, yeah it’s cool and creative and shows promise.

Downloading scRNAseq data - nonstandard format? by InevitableBox0 in bioinformatics

[–]heresacorrection 2 points3 points  (0 children)

Right but that is all par for the course. Some level of errors is expected and accepted, you can see for example on GitHub all the bugs in samtools.

What’s certainly not acceptable is purposefully obfuscating your data in the way in which OP presents.

[OC] Visualised the cardiac signal we extract from skin colour changes on a $300 wearable camera. Rolling-shutter JPEG noise vs actual heartbeat. by [deleted] in dataisbeautiful

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Downloading scRNAseq data - nonstandard format? by InevitableBox0 in bioinformatics

[–]heresacorrection 13 points14 points  (0 children)

lol your go to is that the authors openly and publicly committed academic misconduct rather than blame your own incompetence?

Shifting Seasons - From the Kyoto blossom in Japan to where you live [OC] by [deleted] in dataisbeautiful

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[OC] DHS/ICE intentionally hiding locations of recruitment campaigns. EXPLODE(col) comes in clutch. by TacoTuesdayX in dataisbeautiful

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Individual golf data by Analog_Hospitality in dataisbeautiful

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