Editing the reference sequence

[upendra_35]

I am interested in Reference based transcriptome assembly for my species of interest for which the reference sequence is available from a different accession. For reference based approach i used tophat/cufflinks/gffread to get the final transcript file. Now i am wondering how can i edit the transcript file based on RNAseq information. Basically i don't want the sequence from the reference and all i want is the transcript sequence information based on RNASeq reads.

Any ideas of how to do that?

Thanks