How to generate a transcript sequence derived obtained in the RNAseq?

[super0925]

In RNA-Seq, While we have our list of DE genes, selecting a specific transcript/isoform for gene synthesis is not straight forward. How to generate a transcript sequence derived from a contig of the transcript sequences obtained in the RNAseq experiments? Cheers

[GenoMax]

Are you asking if an overall consensus sequence can be generated for a gene from a set of mapped reads?

[super0925]

Are you asking if an overall consensus sequence can be generated for a gene from a set of mapped reads?

Yep. consensus sequence for each gene could be interesting
Thanks.
How to do that?

[GenoMax]

If you have a linear contig then isn't that the consensus sequence for that transcript or are you referring to a region in the alignment file (where multiple reads are piled up) that you want to derive a consensus sequence from?

[super0925]

If you have a linear contig then isn't that the consensus sequence for that transcript or are you referring to a region in the alignment file (where multiple reads are piled up) that you want to derive a consensus sequence from?

For a particular gene, what is the splice variance ? from Alignment file e.g. bam or sam.

[super0925]

If you have a linear contig then isn't that the consensus sequence for that transcript or are you referring to a region in the alignment file (where multiple reads are piled up) that you want to derive a consensus sequence from?

‘If you have a linear contig then isn't that the consensus sequence for that transcript’
Yes. And how to get the contigs for each?
I want output a sequence as a result of generating a contig from the mapped sequence data. Thank you!