i write because i have a problem with the HUMAnN tool (v3.9 + galaxy1) i used on fecal NGS sequences (samples from four days). I have followed the tutorial “Metatranscriptomics analysis using microbiome RNA-Seq Data”, i got resuls for the “Gene famlilies and their abundance” output with multiple gene families. For the two pathway outputs I only got a coverage of 1.000 and a abundance of 0.000.
The results seem a bit sparse. You are following the steps outlined in this tutorial, correct? Did you run through all steps up to this one the same way as in the tutorial? If not, what was done differently?
If not, what kind of NGS reads are you working with? We have several tutorials to help with community profiles, and can help you to locate a better guide for your reads (probably!) from the choices here.
Or, you can look at a tool like Kraken2 since most read types work with it, and scroll down into where the tutorials that include the tool are located for more ideas.
I am following the steps of the “Metatranscriptomics analysis using microniome RNA-seq data” exactly and up until the pathways determination of the HUMAnN tool everything worked.
I am workling with Illumina short reads to idetify the metatranscriptome of the gut microbiome. And i am not paticularly interested in the taxonomic profile, but rather in the functionallity and differnt pathways.
in the tutorial lists i could not find any fitting tutorials.
For your data, there is either actually no pathway information available for your hits, or there could be some technical issue that could be adjusted to better capture a result. We have another example in this tutorial step if you want to compare approaches. (Note that the downsampled training example didn’t have a pathway identified either!).
