andredsim
commented
2 weeks ago 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
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