Andre Sim

Hi, This seems to be a different error than the first case bambu seems to have worked in this case and finished transcript discovery. Try `print(bambu_out)` to confirm this. As...

Hi, I am glad to hear that worked. I will have to think about why Bambu would crash in the presence of other alignments, because theoretically it shouldn't happen, hopefully...

Hi Asher, Thanks for getting back. I will keep this issue open for now, as I want to either solve the issue in the case its spurious alignments causing bambu...

Hi Asher, I am glad you were able to get it to run. As to why it causes Bambu to fail, I cannot say for certain as as long as...

Hi, Sorry for the delay in replying to this one. Would you please be able to try this branch. This has the changes to the code suggested above. https://github.com/GoekeLab/bambu/tree/HongYhong_fix I...

Hi Sefi, Glad to hear this works. I really need to find the time to update this branch further and get it through a pull request then. @apsteinberg I am...

Hi, For the first code could you show me what list.files(pattern="GV") outputs, is it possible you have another file in your working directory with GV in the name? The second...

Hi, Unfortunately I cannot see it. Was it in your last comment or did you send it another way. Is it possible some syntax might be formatting it in a...

Hi, I have not seen this issue before so I am not exactly sure how to solve it, however here are somethings to try that might circumvent the problem, or...

Hi, All the gene counts being named bambu means it has predicted a lot of novel genes. I believe this is related to the warning I flagged above. As in...