I was trying to analyse my RNA-seq data with TEtranscripts, but I found a problem. The point is that some of my samples have been sequenced using a forward stranded library and the rest of them have been sequenced using a reverse stranded library. As far as I know, you have to indicate a specific library type to analyse all the samples with TEtranscripts. Could you give me a solution? I have been thinking of using only TEcounts separately (one time for forward stranded samples and another for reverse stranded samples), and after that running the differential expression analysis manually with DESeq2.