I am trying to get the read counts for DESeq2 analysis from meta-genomic data. I have assembled contigs using Trinity for all organisms and I would like to map my reads for each sample to these contigs and get the read counts for DESeq2 analysis. Normally for RNAseq we would use GFF file to annotate the read and annotate as a loci, but for metagenomic data, I can't use one specific genome, so I wanted to use Trinity assembled contigs as reference for mapping. However, before proceeding with the read mapping, I would like to annotate each contigs from Trinity. I wonder if I can do BLAST search against
nr. What would be the easiest way to do this? Thanks for your help!