Andre Sim
Andre Sim
Hi, The formatting of your last comment is a bit hard for me to parse (attached picture). From what I gather you are surprised at the results that all the...
Hi, I am not sure I understand your question. Are you able to attach in image or an example of what you mean to better describe it?
Hi both, thanks for reporting this. I was able to replicate this warning using the versions you are using (the version available on Bioconductor at the moment). We currently offer...
Hi, You have a few options here if you would like to do transcript discovery and quantification: 1. You can run bambu using denovo mode where you only provide the...
Hi Sowmya, The first two warnings are more informational, than detrimental to your analysis. The first can occur when there are reads to scaffolds in the fasta file, that have...
Hi Alex, Thanks for using Bambu. I did some digging and I realized that after using prepareAnnotations on TxDb.Hsapiens.UCSC.hg38.knownGene, 16% of the transcripts that do not have a gene id...
Hi Shaowen, How many barcodes do you have? Kind Regards, Andre Sim
Hi Shaowen, With that amount of barcodes/bam files, using the current version of Bambu, you will encounter some computational resource issues. We are currently working on a way to handle...
Hi, Could you share me the script you are using to run Bambu, then I can suggest changes based on what you have already tried.
Hi Sowmya, Here are a few options to do multiple sample analysis when memory is limiting. 1. You can try running all samples together but set `lowMemory = TRUE` 2....