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?
Hi, Bambu needs the alignment of reads to genome, so only the bam file will work. You can use Minimap2 to get the aligned reads (or any other aligner for long reads). If you want to test Bambu with aligned reads, you can follow this short tutorial that uses the SG-NEx samples (which are alrady aligned): https://github.com/GoekeLab/sg-nex-data/blob/master/docs/SG-NEx_Bambu_tutorial.md Thanks!
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version 2.3.6
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!