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Frequently asked Questions

How many replicates should I include in my experiment?

As a rule of thumb we always recommend at least 3 biological replicates for any experiment looking to perform a differential analysis. We also recommend you speak with the Biostatistics department as they would be better at discussing any power calculations you might want to consider before designing your experiment. 

What are the limitations of only doing 1 biological replicate?

If you are unable to perform additional replicates (due to cost, mice, other factors) we will be unable to characterize the biological variation that exists within your conditions and therefore will not be able to compute statistical significance for your study. You will be unable to publish these findings and will drastically increase the likelihood of chasing false-positive findings. Generally, we recommend performing a minimum of 3 biological replicates for a RNA-Seq experiment. We also recommend contacting the URMC Biostatistics Department to discuss statstical power. 

Should I perform paired-end sequencing for my ATAC-Seq experiment?

Yes. Generating paired-end reads for ATAC-Seq fragments allows us to know if your fragments span nucleosomes. It also allows us to computationally evaluate the success of the library prep which is lost when single-end sequencing is performed. This allows us to computationally identify nucelosome positions in your samples and understand if there is any differential nucleosome patterning occurring. The original ATAC-Seq paper: also showed that different types of regulatory elements reside in the nucleosome free  regions (NFR) compared to nucleosome associated regions therefore, fragment size is helpful to filter your data on prior to running motif enrichment analyses. For additional details regarding ATAC and ChIP experiment design please see the following resources: Harvards ATAC-Seq Guidelines Greanleaf's ATAC-Seq Forum

Can I open my RNA-Seq delivered text files in excel?

While we do not recommend working with these files in excel, you can view your data in excel by importing from a text file. We have a tutorial to walk you through how to safely work with gene symbols within excel. 

Can I have your scripts?

No. Our bioinformatics scientists devote a lot of time and intellectual property into designing efficient pipelines. We are happy to share the tools and parameters that we use to enable reproducible work but we will not share our custom scripts and pipelines.

Can you modify the RNA-Seq pipeline to meet our experimental questions?

Yes, we often modify our pipelines to meet the needs of individual experiments. Depending on the amount of effort required there may be an additional service charge that will cover our time to make these project specific changes.

My delivery links don't work anymore, can you help?

Your delivery links no longer work because, for security reasons, they are only live for 7-10 days. We recommend you download all data that we deliver within this window of time. If extenuating circumstances exist that have kept you from downloading the data within this period of time, links can be remade upon request. 

Can the GRC re-analyze my RNA-Seq experiment?

Yes, we request you email us and provide the PI and submission date associated with the project. Project re-analysis will be charged an hourly service fee to cover our bioinformatician's time to re-analyze the data.