Feng Yan

Thanks for you reply. ``` CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions of the genome that are bound by particular transcription factors. It starts by identifying a...

> Hi there, I'm not sure exactly what a full join would look like? Could you provide a simple example? If it makes sense you are more than welcome to...

I use this function to full_join GRanges, might not fit in everyone's case (or maybe everyone has a different definition full_join). I'm sure someone can make it better, so I...

Hi @sa-lee , I will have a try. So this `overlaop_joins_outer` is actually the function `join_overlap_left`? I didn't see any other function in this wrapper. Do you think I should...

Had the same issue, I can understand the pval, as it is the smallest p value that can be achieved under 5000 permutations. But that does not help to identify...

@lauraht Hi, I have similar issues, do you have the answers? And may I ask what parameters you used to match reads in cDNA RNA-seq ONT data? Is the default...

Thank you so much for your reply. Are there any suggestions on how to infer genes from RNA-bloom2 output from your experience? Cheers, Alex

Thank you so much. Would definitely like to have this feature in the future.

> At least it is valid in the test case, again, I am not sure if everyone has the same definition of full_join GRanges.

also interested to know how Salmon uses secondary alignment. Because I found this tutorial https://combine-lab.github.io/salmon-tutorials/2021/ont-long-read-quantification/ actually includes secondary alignments. And based on my experience, secondary alignments are used by Salmon,...