True Stories Researchers Shared With Us - Real Difficulties Getting Bioinformatics Done Right

These are real accounts told to us by researchers we interacted with, reflecting common difficulties in trying to get bioinformatics work done properly-and why reliable support from experienced people can make a big difference.

Story 1: DIY Bioinformatics - It Can Become Quite Messy

Professor A is a well-trained molecular biologist who normally works at the bench. She trusted mature bioinformatics platforms like DNAnexus to analyze her RNA-seq data. At first, things looked simple.

But later, she found that the platform’s normalization failed to adjust for batch effects, and some basic quality control steps-such as checking sequencing depth or identifying outliers-were either missing or couldn’t be customized.

To cross-validate the results, she reran the analysis on a second platform. Unfortunately, the results conflicted with the first one, with very different differential gene expression patterns and pathway enrichments.

She spent several weeks trying to reconcile the findings but couldn’t reach a consistent explanation.

Facing pressure to publish, she submitted the paper anyway-despite knowing the data analysis had unresolved problems. The reviewers noticed right away: they questioned her QC methods, statistical handling, and control for confounders. The feedback was highly critical.

Eventually, she had to shelve the paper and shift focus to other projects, this time seeking more solid bioinformatics support from the beginning.

- Had she involved true experts from the start-people who not only understand the biology but also the computational intricacies-this painful delay probably could have been avoided.

Story 2: Freelancer Gamble - Low Cost Comes With High Risk

Postdoc B was leading a microbiome study, with two papers depending heavily on complex bioinformatics results. Due to budget constraints, he hired a freelancer found online-someone who claimed to deliver fast, affordable analysis.

At the beginning, the freelancer did deliver some results, and B thought they looked fine. But during peer review, serious issues were pointed out: no correction for batch effects, poor handling of multiple comparisons, and lack of proper metadata integration. These are fundamental problems for any microbiome study.

When B reached out for help with the revisions, the freelancer became unresponsive. He stopped replying altogether.

With both papers stuck, and deadlines approaching, B’s funding situation became difficult. He eventually had to change labs and change his research direction-something that affected his entire career path.

- Had he partnered early with a reputable team-people who communicate clearly and provide full support throughout-these problems could have been prevented.

Story 3: Core Facility Bottleneck - Too Many Projects, Too Little Time

Postdoctoral researcher C needed help with a DNA methylation project and went to her university’s bioinformatics core. A junior analyst was assigned to help. But from the beginning, C noticed the analyst wasn’t really engaged with her scientific questions.

The analyst mostly followed rigid workflows-basic methylation calling and DMR analysis. However, her study had a special design, and the analysis should have accounted for that. For example, cell-type heterogeneity and batch bias were never properly addressed.

Later she found out that this analyst had only a few months of training in bioinformatics and only a programming class before that.

After repeated requests, a senior bioinformatician stepped in. But he was extremely busy, juggling many other high-priority projects. As a result, updates became slow and irregular. Her paper was delayed for months.

When reviewers asked for extra methylation analysis and more robust stats, she had to wait even longer-because there was no flexible support to handle those changes efficiently.

- This kind of story is not rare. Many institutional cores are short-staffed or stretched thin. They try their best, but their support is often too rigid or too slow.
- If C had worked with a focused, senior team offering tailored support and enough flexibility, many of these delays could have been avoided.

Story 4: Shell Company Trap - A Nice Website Doesn’t Mean Real Expertise

Postdoc D hired a so-called “bioinformatics company” for ATAC-seq data analysis. The website looked very professional-with detailed service menus, team bios, and attractive prices.

She had a few concerns: the communication was vague, and no clear explanation of the methods was given. But she went ahead anyway, hoping to save money.

Then came delay after delay. The usual ATAC-seq problems showed up: inconsistent peak calling, improper normalization, batch effects not handled, and metadata ignored. Worse, the analysis didn’t address the main biological questions.

When she asked for corrections, the company demanded extra fees to fix their own mistakes.

The manuscript was rejected. Reviewers pointed out poor reproducibility, missing normalization across replicates, and statistical flaws. Later, she found out the company was not what it seemed-it was just a few freelancers hiding behind a fancy-looking website.

- This happens more often than you may think. Many “bioinformatics companies” are actually just freelancers in disguise.
- Don’t be misled by the appearance of a website. Always check credentials, request proof of past successful projects, and make sure the team is transparent and accountable.
- Choosing a reputable, experienced team from the start saves time, money, and frustration.

Story 5: Academic Collaboration - Sometimes It’s Not a Good Fit

Professor E was based at a major academic center and had colleagues working on computational method development nearby. Her lab was generating complex single-cell multiomics data-scRNA-seq plus scATAC-seq-and she hoped to collaborate with one of the local bioinformatics faculty.

At first, it sounded like a perfect match. But soon, problems appeared.

The collaborator’s main focus was on publishing new methods. Professor E, on the other hand, needed her data analyzed in a practical, project-focused way to support her hypothesis and meet grant deadlines.

There were long discussions about authorship, timelines, and direction. The collaborator became busy with other grants and algorithm papers, while Professor E’s project fell behind schedule.

- If your main goal is clear and timely support for your data-not method development or co-authorship negotiation-it may be more practical to partner with a reliable service provider instead.
- At AccuraScience, we focus on one thing: helping you get your project done right, on time, and with confidence.

Why AccuraScience?

•     - Established in 2013, we were the first company in the U.S. dedicated to providing broad-spectrum, customized bioinformatics services.
•     - Our team includes eight Lead Bioinformaticians with a combined 200+ years of bioinformatics research and development experience.
•     - Many of us hold advanced degrees in both biology/biomedicine and computer science, and have served as faculty or bioinformatics core directors at top U.S. institutions.
•     - We’ve completed bioinformatics projects for over 180 organizations across five continents, and are consistently trusted by leading academic and industry researchers for our ethical, secure, and scientifically rigorous practices.

Transparent Pricing

•     - We offer flat-rate, transparent pricing for most projects-based on a clear discussion of your goals and project scope.
•     - You’ll know the exact cost before we begin-we never exceed the quoted price. No surprises. No vague invoices. No billing stress.
•     - Our pricing includes support for peer review at no additional cost, ensuring your results meet publication standards.
•     - Transparent pricing supports confident collaboration and smoother administrative approval.

Long-Term Support

•     - We have been around for 12+ years and continue supporting researcher projects initiated years ago.
•     - We retain full documentation of every project-analysis parameters, key decisions-securely archived in our internal systems.
•     - We can resume your project without missing a step-whether it’s six weeks or three years later.
•     - You continue working with the same Lead Bioinformatician-not someone unfamiliar with the work.

What Sets Us Apart Even Further

Intellectual Engagement

•     - We’re not just technical service providers-we act as scientific collaborators.
•     - We ask the right questions, raise red flags when necessary, and help improve your approach.
•     - Our bioinformaticians think critically about the biological context, not just the code.
•     - Many researchers rely on us to enhance the science itself-not just execute it.

Grantsmanship & Funding Support

•     - We've secured millions in NIH, NSF, and other research grants.
•     - We support analytical sections of grant proposals, methodological justifications, and preliminary analysis.
•     - Our input helps shape compelling, well-supported applications-and continues after funding is awarded.
•     - We understand reviewer expectations and how to deliver data that supports your case.

Data Security, IP, and Institutional Trust

•     - We comply with institutional data handling policies and gladly sign NDAs when requested.
•     - Your data is never shared, repurposed, or reused-ever.
•     - Our internal systems and workflows have passed IT/security reviews at top universities and biotech firms.
•     - We apply the same confidentiality, integrity, and professionalism that researchers uphold.

Continuity & Communication

•     - We maintain institutional memory-including all documentation, files, and decisions-securely and long-term.
•     - You always work with the same lead analyst-no handoffs, no starting from scratch.
•     - We respond clearly, professionally, and promptly-before, during, and after your project.
•     - Researchers value our ongoing engagement as much as our expertise.

Ready to Create Your Own Success Story?

If any of these stories sound familiar, maybe it’s time to work with a team you can count on.

👉 Request a Free Consultation
👉 Meet Our Lead Bioinformaticians
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About the Author: Justin Li earned his Ph.D. in Neurobiology from the University of Wisconsin–Madison and an M.S. in Computer Science from the University of Houston, following a B.S. in Biophysics. He served as an Assistant Professor at the University of Minnesota Medical School (2004–2009) and as Chief Bioinformatics Officer at LC Sciences (2009–2013) before joining AccuraScience as Lead Bioinformatician in 2013. Justin has published around 50 research papers and led the development of 12 bioinformatics databases and tools - including miRecords, siRecords, and PepCyber - while securing over $3.4M in research funding between 2004 and 2009 as PI, co-PI, or co-I. He has worked on NGS data analysis since 2007, with broad expertise in genome assembly, RNA-seq, scRNA-seq, scATAC-seq, Multiome, ChIP-seq and epigenomics, metagenomics, and long-read technologies. His recent work includes machine learning applications in genomics, AlphaFold modeling, structural bioinformatics, spatial transcriptomics, immune repertoire analysis, and multi-omics integration. More at https://www.accurascience.com/our_team.html.