Greetings!
We're using Trinity to do de novo assembly of frog RNA-seq data. From the resulting assemblies, I'd like to be able to identify any transcripts that contain intronic sequences (from partially-spliced transcripts) so that we can filter these out of our data set. Does anyone know of a program that might do this? It would not be a problem for me to put together sets of sequences that represent introns, coding exons, and non-coding exons, in case I need to train a program, e.g. a gene predictor. I fear that predictors will not work well or at all on sequences that are the size of transcripts.
Thanks,
Bob
We're using Trinity to do de novo assembly of frog RNA-seq data. From the resulting assemblies, I'd like to be able to identify any transcripts that contain intronic sequences (from partially-spliced transcripts) so that we can filter these out of our data set. Does anyone know of a program that might do this? It would not be a problem for me to put together sets of sequences that represent introns, coding exons, and non-coding exons, in case I need to train a program, e.g. a gene predictor. I fear that predictors will not work well or at all on sequences that are the size of transcripts.
Thanks,
Bob
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