The Asia RNA Club Symposium will be happening in Seoul in Nov 3-5, bringing together RNA scientists from the Asia-Pacific region. Excellent speakers and a great opportunity to connect! Abstract submission by Sept 5 asiarnaclub.org

Looking forward to the Long-Read Symposium tomorrow! I will be talking about long read RNA-Seq and the SG-NEx Project github.com/GoekeLab/sg-...

We are recruiting! We have an open position for a postdoctoral fellow to join our team at the Genome Institute of Singapore to work with long read RNA-Seq data. It’s a beautiful city state and outstanding research environment! More details here: jglab.org/postdoc-posi...

...reads are only assigned to transcripts after similar cells are clustered into groups, reducing the noise in transcript expression estimates due to missing data. We also provide unique counts for single cells (and EM counts for genes/experiments with high sequencing depth)

The key challenges were dimensionality (>200k transcripts x thousands cells) and estimation of transcript expression. The dimensionality we handle by optimising the representation of reads in memory using barcoded read classes, making transcript discovery and read-to-transcript assignment very fast

The challenge with transcript expression estimation is the limited number of reads per gene, which makes the assignment of (non unique) reads to transcripts difficult. To address this, Bambu performs a clustered EM, in which ....

The dimensionality we handle by optimising the representation of reads in memory using barcoded read classes, which allows fast transcript discovery and read-to-transcript assignment

After a lot of optimisation, we now released the single cell and spatial long read RNA seq module for our transcript discovery and quantification tool Bambu (Bambu-clump) The key challenges were dimensionality (>200,000 transcripts x many thousand cells) and estimation of transcript expression