Chen Ying comments

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                                            Chen Ying

quantification issue

Hi @JintaoL666 , Thank you for using our tool! Please see my answer below: Q1: We are using datasets from the NanoporeRNASeq package where we have generated 6 nanopore RNA-Seq...

Extreme mismatch between JBrowse coverage and Bambu mapping (moderate vs 0 expression)

Hi @gringer , this was caused by one of the bug which we have now fixed in a separate branch that you may use (https://github.com/GoekeLab/bambu/tree/modifyQuant), and with this branch, it...

Extreme mismatch between JBrowse coverage and Bambu mapping (moderate vs 0 expression)

The issue is fixed in modifyQuant branch

Inconsistent read counts within polycistronic transcripts with near-constant expression

Hi @gringer , this scenarios is a bit tricky. In fact, during estimation, for reads that map acorss multiple genes, they will usually be randomly assigned to one of the...

No novel transcripts meet the given threshold

This issue is resolved in modifyQuant branch

Is it possible to get transcript coverage estimates from Bambu?

Hi @bernardo-heberle , this is a good point. We should definitely consider to do that for future release maybe, which probably takes some time to implement. For now, you may...

error with bambu for a big file

Hi @yeroslaviz , following up on Andre's suggestion, you may also try to do the following, - do discovery and quantification separately, - set a specific value to yieldSize, which...

Does the Bam file need to be sorted or unsorted?

Hi @niradsp , yes, the bam file need to be sorted and indexed genome bam file. So you can apply your dataset with bambu directly. As to what is the...

Does the Bam file need to be sorted or unsorted?

yes, we have tested on Promethion datasets on the development branch. You can try with current version first, if not able to run, you can just switch to the development...

Does the Bam file need to be sorted or unsorted?

Hi @niradsp thanks for letting us know the performance of bambu, this is very helpful. I probably know what could be the issue and we fixed it in the development...