Hi, There are 6717 transcripts read into txdb but why GRangesList is only 6550 long? Thanks > txdb <- makeTranscriptDbFromUCSC(genome="sacCer2", tablename="sgdGene") Download the sgdGene table ... OK Download the sgdIsoforms table ... OK Download the sgdCanonical table ... OK Extract the 'transcripts' data frame ... OK Extract the 'splicings' data frame ... OK Download and preprocess the 'chrominfo' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TranscriptDb object ... OK > tx_by_gene <- transcriptsBy(txdb,'gene') > txdb TranscriptDb object: | Db type: TranscriptDb | Data source: UCSC | Genome: sacCer2 | UCSC Table: sgdGene | Type of Gene ID: ID of canonical transcript in cluster | Full dataset: yes | transcript_nrow: 6717 | exon_nrow: 7083 | cds_nrow: 7061 | Db created by: GenomicFeatures package from Bioconductor | Creation time: 2011-04-20 11:20:56 -0400 (Wed, 20 Apr 2011) | GenomicFeatures version at creation time: 1.2.3 | RSQLite version at creation time: 0.9-4 | DBSCHEMAVERSION: 1.0 > tx_by_gene GRangesList of length 6550 $Q0010 GRanges with 2 ranges and 2 elementMetadata values seqnames ranges strand | tx_id tx_name <rle> <iranges> <rle> | <integer> <character> [1] chrM [3952, 4338] + | 122 Q0010 [2] chrM [4254, 4415] + | 123 Q0017 $Q0032 GRanges with 1 range and 2 elementMetadata values seqnames ranges strand | tx_id tx_name <rle> <iranges> <rle> | <integer> <character> [1] chrM [11667, 11957] + | 124 Q0032 -- Best, Zhenjiang