To give an outline of my process so far, I have used DESeq2 on my fq sample files against a trinity de novo assembly to get differential expression values. This gave me a file w/ the gene ids as the Trinity transcript IDs. I then pulled only the Trinity IDs w/ a p-adjusted <0.01 out of the original assembly and ran those in BLAST to ID the significant deferentially expressed genes. My problem is connecting these two sets of data together so I have the expression values together with the gene ID so I can do further downstream analysis.
what have you tried so far to accomplish this? and what 'environment' are you working in, windows, unix, R, ... ?