Hi, can I use “wmgx” workflow (change --contaminate-databases) to analyze metatranscriptomic data? I already got the taxonomic and functional profiling from metagenomes and would like to skip this process in " wmgx_wmtx".
Also, do you know how to include 2 types of contaminate databases (e.g., human transcriptome and ribosomal RNA) when running “biobakery_workflows wmgx”? I tried to add two “–contaminate-databases” but only the last database was used.
Hi, Yes you can do that. To include 2 databases provide them in a comma-delimited list.
Thank you,
Lauren
This is an excellent workaround. I made it to work but raised a question in my mind.
As far as I understood, running wmgx_wmtx workflow helps profiling species content from DNA when we try to map the RNA reads. In this case, we only run wmtx. How does it work? Can we still extract functional activity from the outputs of this cool workaround?
P.S. If we are not focusing on relative contributions to mgx/mtx, viral profiling could be a good application.
@lauren.j.mciver May I know how does the profiling work in this case please?