Andre Sim

Hi Asher, I am glad it was something simple to fix :) Regarding sample names for the summarized experiment object, you can find the sample names on the read class...

Hi Asher, Yes if the default NDR shifts up, it suggests there are more highly ranked non canonical transcript candidates, ranking higher than known transcripts. Its not always because there...

Hi Kenan, Sorry for the late response. The exon number is the the index of the exon within that particular transcript from 1 to n (n is the number of...

Hi Hyeongu, Yes it is possible to use single cell data with the current version of bambu if your only goal is to make a novel GTF. As you said,...

Thanks for reporting this. Did you install Bambu via BioConductor or Github? Was your installation of xgboost separate or part of the dependency installation? If possible I would recommend updating...

The cran version of xgboost is still v1.7.8 (https://cran.rstudio.com/web/packages/xgboost/index.html) which is what bioconductor will install as a dependency I believe. To confirm if thats correct , may I ask if...

Hi, Thank you for reporting the typos in the documentation and error messages. I will have that fixed when we do our next update. You should be able to provide...

Bambu doesn't check the file extension, and as for our purposes .fa.gz, .fastq.gz and .fna.gz are all the same format they should all work so long as include in the...

Hi, You are correct that ncore mainly speeds up the performance when running multiple samples as we distribute each sample to a different core for read class construction and quantification....

Hi, Sorry for the late reply here. I am not 100% certain why this is happening. My guess is that when lowMemory is on, it might be trying to generate...