Hi! I am new to BAMBU and would like to use this for long-read data analysis. The first command line for BAMBU is
test.bam <- system.file("extdata", "SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.bam", package = "bambu")
Is there a way to run BAMBU using fastq file as input too?
Thank you for the reply! I need a gtf output file. I can see it has "extended_annotations.gtf" that contains extended transcript & gene annotations for the genome using long reads data. Do you also have something like "transcript_models.gtf" with constructed transcript models (both known and novel transcripts) for output? If I have extended version, the gtf files contains too much information, including the genome annotation. It would be nice to have just constructed transcripts!