Andre Sim

Hi there, Sorry for the late response. Bambu shouldn't be able to create new ensembl transcript IDs. All novel transcripts will be assigned a transcript id of tx.XXX where XXX...

Hi Alex, There are many things that could influence this. Which parameters are you using for your bambu run and is this a standard long-read run or a custom library...

Hi Alex, This is very strange, if the NDR is 1, you should be getting loads of novel transcripts as that is maximum sensitivity. Could you let me know how...

Hi Alex, The default threshold for min.readCount is 2, meaning only transcripts with 1 full length read are filtered out via this threshold. Your threshold of 5 is therefore less...

Hi Alex, Thanks for sending the rcFile. I havn't finished investigating this, but I will update you with what I have seen so far. I had a look at the...

Hi Alex, Sorry again for the belated response. I was a bit busy the last week and didn't get a chance to investigate this further until today. I found that...

Hi, Since I don't have the bam file its a bit harder for me to troubleshoot, but I will do my best to try and help! Homo_sapiens.GRCh38.105.chr_patch_hapl_scaff.gtf wouldn't work as...

Hi, Sorry about the confusion. checkInputSequence() is an internal function of Bambu so you can run it like so. library(bambu) genome = "genome.fa" genomeSequence

Hi, Ok this all looks good and shouldn't cause the issue. I propose two options. 1. Could you send me test.bam3 so I could troubleshoot it from my end. You...

Hi, no problems that you cannot send the .bam file, I understand there are often limitations on the data. I do want to do my best to solve your issue...