Build TranscriptDB object (txdb.sqlite) ...
Download the refGene table ... OK
Download the hgFixed.refLink 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 TxDb object ... OK
done
Prepare gene/transcript/protein id mapping information (ids.RData) ... done
Prepare exon annotation information (exon_anno.RData) ... done
Prepare protein sequence (proseq.RData) ... done
Prepare protein coding sequence (procodingseq.RData)... done
Warning message:
In .extractCdsLocsFromUCSCTxTable(ucsc_txtable) :
UCSC data anomaly in 433 transcript(s): the cds cumulative length is not a multiple of 3
for transcripts ‘NM_033425’ ‘NM_006510’ ‘NM_001146344’ ‘NM_001010890’ ‘NM_001300891’
‘NM_001300891’ ‘NM_017940’ ‘NM_002537’ ‘NM_003954’ ‘NM_006510’ ‘NM_001278563’
‘NM_001291815’ ‘NM_001359231’ ‘NM_001354658’ ‘NM_001350198’ ‘NM_001243042’
‘NM_001243042’ ‘NM_002570’ ‘NM_001128590’ ‘NM_001271870’ ‘NM_001271872’ ‘NM_001329984’
‘NM_001037501’ ‘NM_001037675’ ‘NM_001277444’ ‘NM_001351365’ ‘NM_001297654’
‘NM_001288952’ ‘NM_001134939’ ‘NM_001301371’ ‘NM_153334’ ‘NM_001348286’ ‘NM_001348208’
‘NM_001348208’ ‘NM_001348208’ ‘NM_001348208’ ‘NM_001348208’ ‘NM_001289152’ ‘NM_199349’
‘NM_138324’ ‘NM_138323’ ‘NM_138322’ ‘NM_138319’ ‘NM_005671’ ‘NM_001143962’ ‘NM_000500’
‘NM_145171’ ‘NM_001318833’ ‘NM_006904� [... truncated]
The CDS and protein data were downloaded from UCSC on the same day with running the following code that had the following warning message: