Hi all,
I’ve been working on a Python-based single-cell pipeline for cross-study integration built around the scverse ecosystem. So far, it works well for 10x Genomics data, but I’m now looking to expand support to other technologies like MARS-seq and SMART-seq.
I am facing some challenges with MARS-seq: using similar QC pipeline to what I use for 10x data (even with adjusted thresholds) seems to be too stringent, I suspect this is due to lower UMI complexity and transcript capture efficiency in MARS-seq compared to droplet-based methods.
SMART pseudo-bulk nature also poses some challenges.
Has anyone here successfully used scverse-based tools on MARS-seq or SMART-seq data? Interested in ways to adapt QC, ambient removal (SCAR particularly) to work with these.
Any insights or examples would be greatly appreciated!
Roy