On these pages you will find basic information about the bio-info facility's infrastructure and how to properly use it to ensure minimum disruptions and maximum productivity. This page also acts as a library of common scripts and templates created to avoid reinventing the wheel then and again. This resource assumes no prior user experience with bioinformatic tools and resources. If you are familiar with the tools and resources, great, if not, please visit the Resources section in the Onboarding tab.
Please use 
For acknowledgements please refer to the text below:
The authors wish to thank the UPSC bioinformatics facility (https://bioinfomatics.upsc.se) for technical support with regards to the RNA-Seq data pre-processing and analyses.
We would also like to acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council, and Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure.
2022/12/06 I found a serious bug in the DE template! I have corrected the DE template: https://github.com/UPSCb/UPSCb-common/tree/master/templates/R, but please check out your analysis done since 2021/03/05. Sadly, it means that any analysis needs redoing! 😞 😞 😞 The issue is that the template used the lfcThreshold when retrieving the DE results (using the DESeq2 results function). What this does, unlike the alpha parameter that sets the FDR threshold to return results, is to change the test that is being done. Instead of comparing for a difference in expression of 0, it tests for a difference in expression at the selected value (+0.5 by default). Results are likely to be quite drastically different!