Long-Read Single-Cell Quality Control and Annotation at CSIC Valencia
From June 7 to July 7, 2026, Eamon McAndrew, LongTREC Doctoral Candidate at IPMC (CNRS, Université Côte d’Azur), had the opportunity to carry out a research secondment at CSIC in Valencia, supervised by Ana Conesa. This secondment offered valuable growth, both in scientific expertise and personal development.
My goal? Learning all about SQANTI-single cell, the Conesa lab’s upcoming tool for the quality control and annotation of long-read single-cell transcriptomes, and assessing its application to my own data. I also aimed to exchange expertise with the host lab on transcript annotation, long-read data quality control and ambient RNA in single-cell long-read data.
Eamon reflects on his experience:
What I Learned 🎓
I gained working knowledge of SQANTI-single cell, which will be valuable for my future work on long-read single-cell data. I also held discussions with experts in the host lab on transcript annotation and long-read data quality control.
Takeaways 🌱
The secondment placed me in Valencia during the LongTREC Summer School (25–27 June 2026), where I taught one day on long-read single-cell transcriptomics. I also gave an oral presentation at the VALT 2026 symposium.
Impact 🌟
A particular focus of my discussions was ambient RNA in single-cell long-read data, which is directly relevant to the quality control methods I am developing. Access to SQANTI-single cell before its release gives me a reference point for evaluating my own QC approach.
Overall, this secondment combined tool training, method exchange and teaching within the network in one month.
