tl/dr; any 1st hand recommendations between these two for simple raw data extracts?

First off, I understand the accuracy and clinical implication of WGS via saliva from these places isn't the best and needs to be taken with a big grain of salt, but IMO as you unravel this science, every single aspect seems to be interpreted vs. simply diagnostic, and basically I can't afford something like prevention genetics as docs won't order it and insurance won't cover it when you're looking for a needle in haystack.

I can afford 500 bux as a first screen though to see if there's something more comprehensive that 23andMe (get your data quick before that place goes fully bankrupt!).

So my main goal is to get the best extracts/formats of raw data for a reasonable cost and if I get some interpretation done for that; awesome-sauce. I'll cut it up and buy independent analysis or take it to a genetic counselor (Which I can get via insurance-funny). Secondly, I'd like to not get screwed around with BS charges, etc. so I'll probably use a virtual credit card anyhow. I don't care about privacy as much as the above. Everything that can ruin me financially has already been stolen repeatedly and I don't know how many more versions of free credit card monitoring I can stand...

The dnacomplete site looks hackish (and has incorrect data comparing their competitors) compared to the nice marketing sequencing has. Sequencing is a little cheaper. DNA complete offers a year membership vs. sequencing's 1 month. I'm struggling to see what either really provides for the cost of the test and I'm not going to be nickel and dimed in a marketplace for basic text str lookups. It wouldn't surprise me if they both use the same lab.

Any recommendations, preferably 1st hand, or links to indepth reviews that are legit?

Thanks in advance.

I built an app that you can search through all published genomics articles on bioRxiv easily

Semantic search and instant AI answers from any published article
Here's a video of how it looks like:

https://reddit.com/link/1ic3upj/video/cuj4bd0o4rfe1/player

Would love to get your thoughts and opinions🤗

https://nouswise.com/

Hey everyone,

I’m working on a population genomics project comparing wild and commercially reared animal populations. I’ve completed variant calling on 6 BioProjects, each with around 80 SRA entries (individual genomes), so now I have VCF files for each genome.

Here’s where I need guidance:

Filtering Individual Genomes: What’s the best way to filter each individual genome before proceeding with further analysis?
I understand that quality metrics (e.g., depth, missing data, heterozygosity) play a significant role, but I’m unsure where to start. Any recommended parameters or tools for filtering these VCFs?

Merging the VCFs:
After filtering the individual genomes, should I merge them?
I’m considering merging them to use tools like vcftools to analyze MAFs, identify sites missing in more than 15% of individuals (to remove them), etc.
Should I merge the VCFs from all genomes (wild and commercial populations) together, or would it make more sense to merge by specific groups (wild vs. commercial)?

Thanks in advance for any advice!

Codegen.eu has been down for maintenance for months now. Is there a similar privacy-friendly wlternative that is actually usable?

Is it worth learning coursera course about it? I'm a biology student from asia who is interested working with genome in the future as a researcher but i don't know how perspective it is in my county. We don't have much research papers published about it

CircleDNA? Nebula Genomics/DNAComplete? Which one gives you the most detailed raw data for further analysis/and or a comprehensive report

It's a arrange marriage thing but I really want to ensure that I can communicate that hey, i am here, and i am willing to learn about your world and if that means talking genomics then be it!!!

I am aware of several genome collections (Decode, Ukbiobank, Truveta). Do you know any such projects where the video of participants is available?

I found that I have rs1800462 genotype CC. Do I understand that this means that it might cause problems with the metabolism of thiopurines?

Hi all,

I’m 27 and have been working as a software engineer for 7.5 years, with experience in software sales. I received my software engineering certificate from General Assembly in 2017. Recently, I’ve become very interested in genetics and am considering transitioning into this field.

Genetics has been a passion of mine for as long as I can remember. I’d often talk to my uncle, who’s a plant geneticist running his own company focused on wheat and oats genetics, about the field. He’d even joke with my dad that I knew more about human genetics than he did! (He works in plant genetics, but my focus is on human genetics.)

I’ve always dreamed of working in genetic technology to help people have healthy offspring, but the time commitment to become a geneticist through medical school feels too long, especially since I’d be almost 40 by the time I’m done.

I’m considering pursuing a more traditional university route, potentially starting with a Bachelor's in Computer Science (which I already have some background in) and then moving on to a Master’s in Genomics or a related field like Bioinformatics or Computational Biology.

I’d love advice on:

• What are the best ways for someone with a CS background to get involved in genomics, bioinformatics, or AI in genetics?
• Are there Master's programs or paths that combine CS with genetic research or personalized medicine?
• How can I leverage my software engineering skills to make an impact in genetics?

I’m eager to use my tech skills in a meaningful way in the genetics field and would appreciate any advice or suggestions!

Three years ago during Covid Genomic companies were being flooded with money from investors. Then the rug was pulled.

Now we are in limbo waiting for the next Chat Gpt-like moment. Of course Fda approvals have occured and diseases have been cured. Progress in genomics is inevitable, in my opinion. Anyone can see the immense investment into genomics with multimillion dollar facilities being built around the United States.

So the question is, what will be the big trigger to show its the future of medicine?

Hi everyone,

I’m currently working on mapping genomes to a reference genome using Minimap2 and have ended up with BAM and BAI files. After the mapping step, I’ve used Samtools and some other QC tools to analyze the data, but I’m a bit unsure about what to do next and whether I’ve missed any important steps.

Here’s an overview of what I’ve done so far:

1. Mapping: I used Minimap2 to map the genomes to a reference genome.
2. QC:
   • Generated stats using samtools stats.
   • Ran Qualimap on each BAM file.
   • Analyzed MAPQ score distribution with awk and samtools view.
   • Extracted depth of coverage using samtools depth.
   • Marked duplicates using samtools markdup.
   • Checked the number of duplicates with samtools flagstat.

I’ve attached an example output from the samtools stats command below for one of the samples:

yamlCode kopieren# Summary Numbers:
raw total sequences: 35320166
reads mapped: 34504872
reads properly paired: 32652872
reads duplicated: 0
reads MQ0: 7515404
mismatches: 63649014
error rate: 1.257102e-02
average quality: 35.5
insert size average: 559.8

Questions:

1. Visualizations: I’d like to visualize the mapping quality, coverage, and any potential issues before moving on to variant calling. What tools do you recommend for this?
2. Next Steps for Variant Calling: Is there anything else I should be doing before moving on to variant calling? Are there specific QC steps I’ve missed?
3. Interpretation: Given the QC report, do you see any red flags or issues that I should address before proceeding with variant calling?

I’m working on an HPC, so any suggestions on tools or efficient methods for visualizing and analyzing my data would be really helpful!

Thanks a lot for your help! I hope I explained everything ok and understandable and I hope this isnt a dumb questions! Thank you in advance everyone!!!!

I'm trying to map both the forward and reverse primer sequences to a reference sequence from NCBI, but every time I run it, the error message '1 read can't be mapped' shows. Does anyone know what I could be doing wrong? the sequences I've put in read sequences are ab1 files and the reference sequence is a fasta file. I've attached a photo of the workflow designer

https://preview.redd.it/emjlzv05nebe1.png?width=2940&format=png&auto=webp&s=3fdd0f41aab7c1abde0e75bb6244e58fb50ca96d

Hi everyone,

I'm planning to create a tool called Pathogen Info Search Tool that lets users search for pathogens and get info on causes, symptoms, treatments, and prevention tips. It’s aimed at biology students and researchers.

Do you think something like this would be useful? Any features you’d want to see?

Thanks for your feedback!

Assuming a constant soil (which is mostly sand) temperature of 20c and a moderate annual rainfall, how long does DNA have until it no longer becomes possible to perform a whole genome sequencing on it?

In other words, for how many years could a DNA sample from a buried body be likely to produce accurate results for a whole genome sequencing in the abovementioned conditions?

I've been finding it surprisingly difficult to find a reputable, working site that generates pharmacokinetics info. I recently received my results from Nebula, and I’ve been looking for a service that ideally shows a large list of medications and its effects. I did the test mainly to gain insight into what psych medications (antidepressants, stimulants) are suitable for me.

- Trying to upload files onto Promethease just shows an error message. It seems to be dead based on this recent thread,

- Codegen.eu shows website undergoing rebuild,

- Nutrahacker's Pharmacogenetics Panel PGx is exactly what I'm looking for (their demo here), but at $300 its way too expensive,

- And I’ve looked at Genetic Genie’s drug response section, but it’s quite difficult to interpret and I can’t seem to find explanations for most of the listings.

Looking further, I’ve found MyGenomeRx, Gene2Rx, and PharmHand. If you know anything about these sites or any others, it would be helpful to hear about your experience. Any insights or recommendations would be greatly appreciated, thank you!

I have a number of areas interspersed on the q arm of my Y chromosome with extremely poor mapping (most reads with MQ = 0 ). These are in male-specific areas (q11.222, q11.223, q11.23) with a number of protein-encoding genes important for fertility (I'm a single M, never married, no kids, never attempted to conceive so have no idea of my fertility status). Both Nebula's 100x and Sequencing's 30X show the same poorly mapped areas in the CRAM/BAM file in IGV. Most of the q12 region is completely missing data. Is there just something about the Y chromosome that is difficult to sequence, or does this indicate potentially real deletions in my Y chromosome?