The bioBakery help forum

Understand Additional type -t parameters

Hi @fbeghini
I have a few questions again regarding the additional analysis and arguments:

  1. If I want normalized output profiles(normalized in terms of metagenome sizes of fastq files) then would it be okay to use *marker_ab_table?

  2. –nreads: I have paired end fastq files and suppose that forward end file has 70 reads and reavers end has 70 so shall I put --nreads as 140 or just 70?

Thanks
Saraswati

  1. Yes
  2. If they are used as single end (both are passed to MetaPhlAn by comma-separating the file names), you need to keep 70