Hello,
After running METABOLIC I open up the main results file (METABOLIC_result.xlsc) to check what metabolisms are present. My question is understanding the discrepency between the Presence/Absence determination in the sheets and the KEGGModuleStepHit sheet. For example, why are only some steps of a pathway given abundances in the HMMHitNum sheet and not all the steps listed in the KEGGModuleStepHit sheet for that pathway? For example, for the Calvin Cycle, only Rubisco Form l and ll are listed with counts in the HMMHitNum sheet but the rest of the pathway as outlined in the KEGGModuleStepHit sheet is not listed along with its associated counts? I would like to know the counts for each gene in my pathways of intererst so that I may determine not only if the pathway is present but also its relative abundance.
Thanks,
Hello,
After running METABOLIC I open up the main results file (METABOLIC_result.xlsc) to check what metabolisms are present. My question is understanding the discrepency between the Presence/Absence determination in the sheets and the KEGGModuleStepHit sheet. For example, why are only some steps of a pathway given abundances in the HMMHitNum sheet and not all the steps listed in the KEGGModuleStepHit sheet for that pathway? For example, for the Calvin Cycle, only Rubisco Form l and ll are listed with counts in the HMMHitNum sheet but the rest of the pathway as outlined in the KEGGModuleStepHit sheet is not listed along with its associated counts? I would like to know the counts for each gene in my pathways of intererst so that I may determine not only if the pathway is present but also its relative abundance.
Thanks,