Hello,
I am running my metagenomics raw data in Galaxy Europe and I am facing trouble with the HumanN. I have selected Locally cached for the Database with clade-specific marker genes which ended up error showing “please provide a value for this option:”.
Alternatively, please let me know if I need to select from History and add my Megahit data.
Thank you for your help in advance.
Jawahar
1 Like
Welcome, @jawaharrajk
Yes, you’ll need to supply that content from the history.
Inputs
HUMAnN can start from a few different types of input data each in a few different types of formats:
-
Quality-controlled shotgun sequencing reads
This is the most common starting point : A metagenome (DNA reads) or metatranscriptome (RNA reads) -
Pre-computed mappings of reads to database sequences
-
Pre-computed (typically gene) abundance tables
HUMAnN uses 3 reference databases Locally cached databases have to be downloaded before using them (using the dedicated tool). Custom databases can also be used after upload.
Hello,
Thank you very much for your reply. Could you also suggest to me how to download the 3 reference databases Locally cached databases?
Thank you
Hi @jawaharrajk
Since you are working at a public server, and are not admin, the data manager cannot be used to index any locally cached databases. I will tag this as a request but that will not happen immediately and you shouldn’t wait.
Instead, get the data into the history and use them as custom databases from the history.
Links to the tool author’s publication and resources are down a bit further on the tool form below the help I posted.
Hello @jennaj
Thank you very much for your suggestion. Also, I have some doubts about editing a workflow for metagenomics. Could you please help me with this?
Thank you
Jawahar
Each tutorial has an example, and how to create and customized workflows is covered in a different set of tutorials.
See Galaxy Training!
And many of those same tutorials were grouped together in a learning suggested order at Advanced Galaxy Features