CoverM abundance calcaulation

1

Hi all,

I’m looking for advice on calculating RPKM or TPM values to estimate gene abundance from metagenomic data in Galaxy.

My current plan is:

  1. For each sample, obtain contig abundance (contigs were assembled using CLC Workbench).

  2. From this, estimate the abundance of antimicrobial resistance genes.

I’ve seen that the coverm contig function in the tool CoverM can be used for this step.

Could anyone advise on the recommended parameters or workflow in Galaxy to go from contig abundance to gene abundance?

Thanks in advance!

2

Hi @cec_l ,

The best option is a published protocol or protocol used by someone else.

Maybe check tutorials on Galaxy training network: Galaxy Training!

For example, Hands-on: Antibiotic resistance detection / Antibiotic resistance detection / Microbiome

Kind regards,

Igor