getting the test results of multiple transcripts; even though, I am using gene-level analysis

Question

[Fawzi Yassine]

Hi, I am using RNAseq analysis to find genes differentially expressed between 2 conditions. I am using StringTie for transcript assembly and quantification.
In ballgown (gene-level) or deseq2 I am getting the test results of multiple transcripts for many genes. Why is that so knowing that I am using gene-level analysis not transcript-level one? Regards,

[ATpoint]

From what I understand you ran stringtie and then did some expression analysis, but how? DESeq2 is intended for gene level analysis, so you must aggregate the transcript level counts of stringtie to the gene level, e.g. with [tximport] (link). Did you do that? It seems you did not, otherwise you would not get multiple transcripts in the results. How did you perform gene-level analysis in ballgown? Your post lacks details.

[h.mon]

Please edit your post to include the commands you used - we have no idea of what you did, parameters chosen, and so forth.