Alex and Lorena discuss a large bulk RNA-seq project that yielded lasting changes to their group’s everyday bioinformatics practices via the creation of parameterized R Markdown code templates. In the “Quick Sip” segment, they discuss reticulate (https://rstudio.github.io/reticulate/) for managing python environments in an R context, and in “Brewing Up Answers”, they reflect on the differences between industry and academia bioinformatics.  Thanks to our 300+ listeners of past episodes! Send us your comments, questions, and suggestions using this form: https://forms.gle/ncwo6HZeN4uA9gPg7 Also, we are looking for sponsors! Please get in touch if you or your business would like to help support this podcast. Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/ If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1 Hosted by Ausha. See ausha.co/privacy-policy for more information.

In this episode of A Coffee with CompBio, Lorena and Alex share the twists and turns of realizing their methylation data wasn’t what it seemed. From puzzlingly low mapping rates to unexpected cloud costs caused by unoptimized compute jobs—thankfully caught just in time thanks to cost alarms—they highlight how essential clear communication and bioinformatics-aware experimental design are to any successful project. In our new segments, Quick Sips and Brewing Up for Answers, we talk about PIXI (https://pixi.sh/latest/) for managing software environments and dig into the ever-present challenge of staying organized across complex projects. Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7 Also, we are looking for sponsors 💰! Please get in touch if you or your business would like to help support this podcast 🙏. Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/ If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1. Hosted by Ausha. See ausha.co/privacy-policy for more information.

In our first episode, Alex and Lorena dive into the messy reality of processing single-cell RNA-seq data. What started as a simple QC project turned into a week-long journey across compute environments, mysterious pipeline errors, and zero-cell outputs. Along the way, we troubleshoot issues with Cell Ranger, uncover strange sequencing artifacts, and reflect on lessons in data handling, pipeline reproducibility, and client communication. Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/ If you enjoyed the episode, please subscribe and leave us a review. Hosted by Ausha. See ausha.co/privacy-policy for more information.

In the introductory episode, Lorena and Alex introduce themselves and share how they got started in computational biology. They talk about their career paths, what drew them to bioinformatics, and some of the challenges and surprises they’ve encountered along the way. They also give a preview of the kinds of topics and practical issues they’ll be covering on the podcast, from workflow basics to troubleshooting analysis hiccups. Hosted by Ausha. See ausha.co/privacy-policy for more information.