In differential expression analysis using ballgown, how do we know that genes are upregulated or downregulated in control or treatment?

Question

[Vikram]

This is an image of file containing differential expression data, here column named "fc" stands for fold change, But I'm not sure if according to control or treatment the fold change is calculated?

Any suggestions will be appreciated!

Thank you in advance!

[ATpoint]

Just to be sure, are you doing differential transcript or gene expression analysis? Do you really need stringtie? Is this a well-annotated model organism? It can well be that a much simpler pipeline than hisat-stringtie-ballgown that is meant for gene- rather than transcript level will get much better results. Please clarify.

[Vikram]

I am conducting differential gene expression analysis. Regarding the bioinformatics pipeline, I have chosen to use StringTie somewhat arbitrarily. The genome of the organism under study is well-annotated. . However, I am unsure if other pipelines might be more suitable or efficient for this particular analysis. I would appreciate any guidance or recommendations you might have regarding alternative pipelines that might produce better results. Thank you

[ATpoint]

Just take your alignment (bam file), quantify against a reference GTF file with featureCounts and analyse with DESeq2. That is much more suited for DEG analysis than stringtie and ballgown. DESeq2 has great documentation.