Multiple blast hits per transcript/peptide sequence.

Question

[4117837]

Hi there

I am using the Trinotate pipeline to annotate a transcriptome assembly. I have 69 000 transcript sequences. Blastx returned around 6 million hits and blastp returned around 4 million. Looking at the output, there are multiple hits per transcript/peptide sequence. When continuing with annotation, should I retained just the top hit for each transcript and peptide? I set the E value to 0.0001

I