Uniquely mapped reads and differential expression analysis with Trinity

Question

[seta]

Hi all,

As far as I know the reads with unique mapping should be considered for counting and doing differential expressed gene analysis. However, the uniquely mapped read percentage during mapping back to transcriptome assembly made by Trinity is very low (usually about 25-30% for me), In some papers (not all), it's mentioned that the redundancy was removed for transcriptome assembly and just uniquely mapped reads were considered for the DEG analysis. Could you please let me know your opinion about using only uniquely mapped reads for DEG analysis, also your suggestion for removing redundancy from Trinity assembly would be highly appreciated.