Error in map_data function

[cmarti]

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]

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]

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