I'm trying to normalise gene counts (estimated using Bowtie2 mapping) of PROKKA annotated contigs generated from a metagenome dataset. I would like to use gene length (bp) for this normalisation since the counts mapped to a particular gene will be affected by its length and I need to perform some gene-to-gene comparisons in my dataset. Where could I obtain the gene length of reference sequences used by PROKKA for the functional annotation? Should I explore the different databases? Do they all have gene length information?
Hi there,
I'm trying to normalise gene counts (estimated using Bowtie2 mapping) of PROKKA annotated contigs generated from a metagenome dataset. I would like to use gene length (bp) for this normalisation since the counts mapped to a particular gene will be affected by its length and I need to perform some gene-to-gene comparisons in my dataset. Where could I obtain the gene length of reference sequences used by PROKKA for the functional annotation? Should I explore the different databases? Do they all have gene length information?
Thanks, Miguel