Metatranscriptomic pre-processing

Infrastructure and utilities bioBakery workflows
1

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.

2

Hi, Yes you can do that. To include 2 databases provide them in a comma-delimited list.

Thank you,
Lauren