Alexander J Ritter

Hey Andre, No worries, I got that part figured out. But I do have another question: I’ve been trying out different cutoffs for de novo isoform detection and no matter...

Hey Andre, Below is an example of how I'm running Bambu. For "x", I tried 0.01, 0.05, 0.10 (default), 0.25, 0.50, 0.75 and 1.00. The "bam_file" is from a standard...

Hey Andre, I was getting novel transcripts with min.readCount = "/some/output/directory/here" to your arguments. This should output an > .rds file which contains all the read classes for your sample...

Hey Andre, Right, I tried several different min.readCount and min.readFractionByGene cutoffs from more to less stringent and like I said I was able to detect just a few novel transcripts...

Do you think it's possible that many/all of the novel transcripts just aren't being included in the output from writeBambuOutput()? Because I'm primarily looking at the transcript counts and the...

Awesome, thanks for checking all that, this is very helpful! On Sun, Sep 4, 2022 at 8:53 PM Andre Sim ***@***.***> wrote: > Closed #300 as completed. > > —...