Let's say I have a candidate gene and I believe that in an individual sample, the genome sequence differs from the reference which then interferes with alignment.
Is there a way for me to do a "transcriptome assembly" with a specific read or sequence as a starting point? And only do the k-mer assembly from that single sequence?
I could probably code something myself but I feel like a tool to do this must already exist?
The goal here is to avoid the significant overhead of assembling a whole transcriptome when I'm only interested in one gene.
NOTE: In this case the data is RNA-seq