Clarification in the workflow steps of the RNA-seq analysis for differential gene analysis

Question

[amy16]

Hi all, I am using Stringtie for transcript assembly and quantification. My experimental design includes 4 different genotypes each under two treatment conditions with sim to identify differential gene expression analysis. I did the sequence alignment to the reference genome and the used Stringtie to assemble the transcripts. I am not clear about the --merge function in stringtie. Which GTF files should I use to merge the transcripts?? After running the initial stringtie function for transcript assembly, there are these following output files, B1C_transout.gtf and B1C_cov_refs.gtf for each sample. Do I merge these two GTF files?? And then estimate the expression values to generate the CTAB files??

-Thanks

[GenoMax]

StringTie's merge function

[amy16]

Thanks for directing me!!!!