Hi. I'm sorry for stupid question, but I'm new to BioIT. I've made ballgown ready files with stringtie at the end of the process of counting genes expression and gene_count_matrix.csv with prepDE.py. And now the problems begin. When i've used DESeq2 for calculating stats for my gene_count_matrix i decided to merge outcome with ballgown table with filtered out covs (team needs only FPKMs). And i noticed, that some genes are (i guess "made by"? I'm no biologist so i don't know how it works) by different transcripts. This multiplies the amount of outcomes and team said, that's something is wrong here. How to make it work? My initial thought was to just merge rows with the same gene_id and ignore transcript, but ballgown table contains of FPKMs and not raw gene expression data and it seems to me, that this method is wrong. Maybe I'm mistaken (God i hope I'm mistaken, because it would be the easiest thing to do), but from my mathematical point of view data that has been somehow processed, should not be summed just like that. Thanks for reading and for answers in advance! Cheers!
