how to handle isomIRs in small RNA sequencing analysis

Question

[hannah]

Hi I am new to small RNA sequencing so apologies if this is a stupid question..! I have data from an experiment where cells were treated with different compounds and then small RNA sequencing was performed. The analysis was done using the small RNA app on illumina basespace (not by me..). Now I have a list of counts and DE of mature miR sequences and a huge number of isomiRs. Should I present the mature miR and isomiR data separately? Or should I try to collapse the isomiRs so they are all counted as one miR...e.g the reads of 10 different isomIRs of miR-29a would not be considered separately but all under the umbrella of miR-29a? If I should do the latter- I would be very grateful for some help on how I would do that! Many thanks