I have transcript assembly and I have tried to annotate to human Ensembl cDNA through tblastx. I got blast top hits in Ensembl transcript id. I have converted these top hits Ensembl transcript id to Ensembl Gene id through Biomart tool. But now I have many transcripts match to same gene. If I have to consider one transcript for each gene what criteria can I choose? Whether based on transcript length or any other criteria?
Ensembl Gene ID Ensembl Transcript ID ENSG00000139618 ENST00000380152 ENSG00000139618 ENST00000530893 ENSG00000139618 ENST00000528762 ENSG00000139618 ENST00000470094 ENSG00000139618 ENST00000533776 ENSG00000139618 ENST00000544455
In the above example which Ensembl transcript id can I choose for the gene ENSG00000139618?