Removing uncovered transcripts from multi FASTA reference file

Hi everyone 🙂

for RNASeq analyses, I have a reference file, containing multiple transcript sequences (it´s a subset of the NCBI human hg38 transcriptome). I found, that some of the transcripts are not even covered by a single read (especially if there are several transcript variants) and would like to exclude them from the file. Is there a way how I could filter those sub-FASTAS of my FASTA, that are covered by less than X reads?

I tried to search for an answer, but didn´t find any helpful posting, yet.

Thanks a lot in advance and have a nice day 🙂