How To Modify A Reference Based Transcriptome Assembly?

Question

[upendrakumar.devisetty]

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

[Damian Kao]

You want to extract transcript sequences from the reference genome based on assembly annotations generated by tophat/cufflinks?

[upendrakumar.devisetty]

No i have already done that. Now i have final transcript file but the problem is the sequence of the transcript file is from the reference and not from my RNAseq reads which i don't want because it is from a different accession.

Answer 1

[Istvan Albert]

If you need a fully de-novo transcriptome assembly that does not incorporate other information then you should create it as such. You cannot later remove information used in the assembly, nor can you reverse engineer to undo the effects of including the reference.