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huangyh09 / brie

BRIE: Bayesian Regression for Isoform Estimate in Single Cells
https://brie.readthedocs.io
Apache License 2.0
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Error in map_data function #25

Closed cmarti closed 5 years ago

cmarti commented 5 years ago

Hi,

I have been trying to use BRIE for a couple of days and running into errors when trying to quantify splicing rates following the manual. In particular I was getting an error in the MH_heuristic function because idxF was empty. I have tracked down this to the map_data function:

"elif ids[idx1[i]] == tran_ids[idx2[j]]:"

this basically never happens because of the suffixes you add to the ids. I have modified my version to remove the suffixes but I am not sure this is how it should be done. Anyway, have a look please and see if you can fix it.

Thanks!

cmarti commented 5 years ago

I sorted it out. Apparently the event filtering step changes the format of the annotation file and only the new GTF format is compatible with the downstream BRIE analysis. It is a bit confusing though, I would expect to have the same formats along the pipeline.

huangyh09 commented 5 years ago

Hi, Thanks for updating and good to hear it is sorted. This confusing issue will be taken into account and hopefully sorted in new release. Thanks Yuanhua