I found a few zero-length exons in GENCODE... Does anybody know if that is a bug, or if it has a meaning ?
zcat gencode.v25.annotation.gtf.gz | awk '$3 == "exon" && ($5 - $4) == 0' | cut -f1,2,3,4,5,7,9 | cut -c1-65 chr2 ENSEMBL exon 96695297 96695297 + gene_id "ENSG00000249715.9" chr2 ENSEMBL exon 166473892 166473892 - gene_id "ENSG00000136546. chr4 ENSEMBL exon 1730388 1730388 + gene_id "ENSG00000013810.18"; chr4 ENSEMBL exon 169663114 169663114 + gene_id "ENSG00000109572. chr5 ENSEMBL exon 796064 796064 - gene_id "ENSG00000188818.12"; t chr5 HAVANA exon 88804598 88804598 - gene_id "ENSG00000081189.14" chr11 ENSEMBL exon 71580167 71580167 - gene_id "ENSG00000204571.5 chr11 ENSEMBL exon 76191778 76191778 - gene_id "ENSG00000085741.1 chr11 ENSEMBL exon 101050949 101050949 - gene_id "ENSG00000082175 chr14 ENSEMBL exon 24632719 24632719 - gene_id "ENSG00000100453.1 chr16 ENSEMBL exon 89553267 89553267 + gene_id "ENSG00000197912.1 chr17 ENSEMBL exon 41624191 41624191 - gene_id "ENSG00000128422.1 chr17 ENSEMBL exon 43883386 43883386 - gene_id "ENSG00000108852.1 chr18 ENSEMBL exon 9887458 9887458 + gene_id "ENSG00000168454.11" chr19 ENSEMBL exon 49836839 49836839 + gene_id "ENSG00000104973.1