Hi,
I am trying to assemble the transcriptome of a highly heterozygous species that may also be a tetraploid. I am using Trinity for that purpose, and was wondering how the program differentiates whether two highly similar transcripts constitute two different isoforms or two different genes altogether?
I have noticed that the isoforms tend to have small differences (SNP/small deletions) but am not sure what the threshold is, if at all, for calling a similar transcript a new gene?
Any thoughts would be appreciated.
Thanks
I am trying to assemble the transcriptome of a highly heterozygous species that may also be a tetraploid. I am using Trinity for that purpose, and was wondering how the program differentiates whether two highly similar transcripts constitute two different isoforms or two different genes altogether?
I have noticed that the isoforms tend to have small differences (SNP/small deletions) but am not sure what the threshold is, if at all, for calling a similar transcript a new gene?
Any thoughts would be appreciated.
Thanks