Multiple hits per transcript/peptide after blastx and blastp

[tann5er]

Hi there

I am using the Trinotate pipeline to annotate a transcriptome comprising of 70 000 transcripts. After running blastx and blastp, i got 6 million and 4 million hits, respectively. This is due to there being multiple hits per sequence. Do I first have to filter and keep the top hit for each sequence to continue with the pipeline?

Kind regards,
Tanner