I am in need of some advice.
Background: I have performed a genome-guided transcriptome assembly by aligning multiple RNAseq reads to a reference genome using HiSAT2 and assembling using StringTie. I then use TransDecoder to obtain the CDS of these transcripts. From these, I have identified a few transcripts of interest (candidate genes), however, quite a few of these are fragmented/incomplete.
My question is as follows: Is there a way of obtaining complete CDS of these transcripts of interest by using the above-mentioned resources? I'm wondering if it would be possible to map reads to these transcripts of interest and then try to reassemble using the mapped reads..has anyone tried such an approach?
Any reading material on the topic would also be very much appreciated.