I observed that in the output matrix of bustools count, there's no eq class with ID = 0, they begin with 1. after matching the text output of bustools sort and with the .mtx output of bustools count, I can say that a +1 is added to all eq class IDs. But the corresponding EC to TX map (outputted from bustools count) still contains eq class ID of 0.. Could anyone please clarify this?
Also, could you please confirm whether the UMI counts are collapsed per eq class (set), or per gene, when I use the option --genecounts ?
I am using Bustools v 0.39.3 for correct/sort and the devel branch for count.
I observed that in the output matrix of
bustools count, there's no eq class with ID = 0, they begin with 1. after matching the text output of bustools sort and with the .mtx output ofbustools count, I can say that a +1 is added to all eq class IDs. But the corresponding EC to TX map (outputted frombustools count) still contains eq class ID of 0.. Could anyone please clarify this?Also, could you please confirm whether the UMI counts are collapsed per eq class (set), or per gene, when I use the option
--genecounts?I am using Bustools v 0.39.3 for correct/sort and the devel branch for count.