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 - ThreadSky

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jonathangoeke.bsky.social • 120 days ago

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

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jonathangoeke.bsky.social•120 days ago

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

jonathangoeke.bsky.social•120 days ago

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 ....

jonathangoeke.bsky.social•120 days ago

...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)

jonathangoeke.bsky.social•120 days ago

The recommended way to run bambu-clump is through the nextflow pipeline (bambu-pipe), which optimises barcode detection, alignment, transcript discocery and quantification, and it also includes an option to identify fusion transcripts in single cells https://github.com/GoekeLab/bambu-singlecell-spatial

jonathangoeke.bsky.social•120 days ago

This work was down by Andre Sim, Min Hao Ling, Chen Ying, Sui Yue, together with Jay Shin's team at GIS. Let us know your comments and feedback, we aim to improve Bambu with every release! https://github.com/GoekeLab/bambu

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