Andre Sim

Yes this would be possible. This is how low_memory mode is meant to work, albeit it still needs to load the whole bam into memory. There are 2 caveats to...

Hi Sowmya, Yes that looks fine. With regards to visualization it depends on what you are wanting to see, and there are lots of packages available for plotting the granges...

Hi Matthias, In most typical use cases you do not need to worry about the model being used as it should train on the data you provide it. To answer...

Hi Sowmya, In our pipelines we do not do any extra filtering or QC and use the minimap2 output directly. We do purposely keep supplementary reads in, in the event...

Hi, I cannot be sure without seeing the results, but my best guess is that these 125,254 annotations are reference annotations that are not expressed in your sample. Bambu does...

Hi Yuyun, We discussed this internally to try and determine why you are getting these results. We came up with the following: 1. We recently released a new version (3.4.1...

Hi Yuyun, Thanks for sending this, this was helpful to help us rule out a few possible reasons. Did running Bambu with the latest version change the results? If not,...

Hi Yuyun, Sorry for the delayed response. This is very odd you are getting the error that the assignDist parameter is not there, as it has been in our Bambu...

Hi Yuyun, Very sorry I made a mistake earlier. We actually renamed assignDist to returnDistTable, and I forgot about that change. Could you please try rerun it with that instead....

The error Error in (function (cond) : error in evaluating the argument 'x' in selecting a method for function 'bfcnew': Failed to collect lazy table. Caused by error in `db_collect()`:...