See instructions for Example 4 at this site -- https://genome.ucsc.edu/goldenPath/help/bigGenePred.html
Note that my files are not in gff3 format, so use the gtf instructions.

mkdir working;

/ddn/gs1/home/grimmsa/tools/ucsc/gtfToGenePred -genePredExt data/GATA3_PacBio_isoforms-21jan2022-ClassA.gff working/ClassA.genePred;
/ddn/gs1/home/grimmsa/tools/ucsc/genePredToBigGenePred working/ClassA.genePred working/ClassA.bigGenePred.txt;
sort -k1,1 -k2,2n working/ClassA.bigGenePred.txt > working/ClassA.bigGenePred.sorted.txt;
/ddn/gs1/home/grimmsa/tools/ucsc/bedToBigBed-v.2.9 -type=bed12+8 -tab -as=/ddn/gs1/home/grimmsa/references/ucsc/bigGenePred.as working/ClassA.bigGenePred.sorted.txt /ddn/gs1/shared/dirib/reference_genomes/hg38/hg38.noAlt.chromSizes data/GATA3_PacBio_isoforms-21jan2022-ClassA.bb;

/ddn/gs1/home/grimmsa/tools/ucsc/gtfToGenePred -genePredExt data/GATA3_PacBio_isoforms-21jan2022-ClassB.gff working/ClassB.genePred;
/ddn/gs1/home/grimmsa/tools/ucsc/genePredToBigGenePred working/ClassB.genePred working/ClassB.bigGenePred.txt;
sort -k1,1 -k2,2n working/ClassB.bigGenePred.txt > working/ClassB.bigGenePred.sorted.txt;
/ddn/gs1/home/grimmsa/tools/ucsc/bedToBigBed-v.2.9 -type=bed12+8 -tab -as=/ddn/gs1/home/grimmsa/references/ucsc/bigGenePred.as working/ClassB.bigGenePred.sorted.txt /ddn/gs1/shared/dirib/reference_genomes/hg38/hg38.noAlt.chromSizes data/GATA3_PacBio_isoforms-21jan2022-ClassB.bb;

/ddn/gs1/home/grimmsa/tools/ucsc/gtfToGenePred -genePredExt data/GATA3_PacBio_isoforms-21jan2022-ClassC.gff working/ClassC.genePred;
/ddn/gs1/home/grimmsa/tools/ucsc/genePredToBigGenePred working/ClassC.genePred working/ClassC.bigGenePred.txt;
sort -k1,1 -k2,2n working/ClassC.bigGenePred.txt > working/ClassC.bigGenePred.sorted.txt;
/ddn/gs1/home/grimmsa/tools/ucsc/bedToBigBed-v.2.9 -type=bed12+8 -tab -as=/ddn/gs1/home/grimmsa/references/ucsc/bigGenePred.as working/ClassC.bigGenePred.sorted.txt /ddn/gs1/shared/dirib/reference_genomes/hg38/hg38.noAlt.chromSizes data/GATA3_PacBio_isoforms-21jan2022-ClassC.bb;

/ddn/gs1/home/grimmsa/tools/ucsc/gtfToGenePred -genePredExt data/hq-filtered-version_18jan2022.only_PB.12563_GSE1.gff working/GSE1.genePred;
/ddn/gs1/home/grimmsa/tools/ucsc/genePredToBigGenePred working/GSE1.genePred working/GSE1.bigGenePred.txt;
sort -k1,1 -k2,2n working/GSE1.bigGenePred.txt > working/GSE1.bigGenePred.sorted.txt;
/ddn/gs1/home/grimmsa/tools/ucsc/bedToBigBed-v.2.9 -type=bed12+8 -tab -as=/ddn/gs1/home/grimmsa/references/ucsc/bigGenePred.as working/GSE1.bigGenePred.sorted.txt /ddn/gs1/shared/dirib/reference_genomes/hg38/hg38.noAlt.chromSizes data/hq-filtered-version_18jan2022.only_PB.12563_GSE1.bb;