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GoekeLab / bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data
GNU General Public License v3.0
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Output counts grouped by a cell barcode field in BAM file? #301

Closed danledinh closed 2 years ago

danledinh commented 2 years ago

Output counts grouped by a cell barcode field in BAM file?

andredsim commented 2 years ago

Hi,

Sorry for the late reply. I am not sure exactly what you are asking for but I will do my best to try and answer.

If you already know the read - cell assignment. You can use the trackReads = TRUE option in bambu to produce a read-to-transcript map. This would allow you to map the barcodes from the reads directly to the transcripts.

Bambu currently doesn't use and cell barcodes during its processing.

If this doesn't answer your question let me know and I can reopen the issue.