Make novel GTF from single cell data using bambu

[hyeon9]

Thank you for your highly intuitive and accurate tool!

Recently, I plan to apply Bambu to my single cell RNA sequencing data to get transcriptome information. So, as I think, it is possible to construct transcriptome based on my merged bam and retain only transcripts with non-zero expression in extended gtf file. I'm wondering whether this approach makes sense.

Thank you, Hyeongu

[andredsim]

Hi Hyeongu,

Yes it is possible to use single cell data with the current version of bambu if your only goal is to make a novel GTF. As you said, you want to use the merged bam and if you want to remove transcripts where you didn't find any full-length support you can filter out those with non-zero full length counts.

We are planning to release a single-cell capable version of bambu soon but it is currently in the beta phase at the moment.

Kind Regards, Andre Sim