goldenflaw

Do you have XS tags in your alignment bam files? I suspect your alignment might not contain this information. Yang On Wed, May 3, 2023, 08:07 NufarGrinshpan ***@***.***> wrote: >...

Thank you Drevansa! We will consider these in the next release. Best, Yang On Sun, Jun 3, 2018 at 12:47 PM drevansa wrote: > Hello, > > I have a...

Thanks for pointing this out. We are working on a newer version of LeafCutter with these fixes. Best, Yang On Sun, Dec 18, 2022, 18:43 Aniketh Janardhan Reddy < ***@***.***>...

Thank you, this note has been noted and we will fix this, along with other requests in an upcoming leafcutter release. Best, Yang On Wed, Apr 12, 2023 at 11:56 ...

I'm afraid there is no good explanation for this. It just works empirically, i.e. it yields more qtls at the same FDR. I suspect that it might help get rid...

I believe there has been other reports that some of the parameters in leafcutter do not work as intended, including when reducing the minimum number of reads too much. We...

Hi Vitor, This may be an edge case which we will try to fix in future versions. For now, if you already know which junction/cluster you are interested in. You...

Thanks for this Austin. My lab is working on a new version of LeafCutter with added functionality. We will keep this in mind, but we likely won't be ready for...

@jackhump Could you move your scripts/leafcutter_cluster_regtools.py to clustering/? Seems you updated it last.

Hmm, I thought I had fixed it.. In any case. It really depends on your use case. If you call sQTLs, I would use looser cutoffs. Best, Yang On Mon,...