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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

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    $\begingroup$ What did you mean by genome sequence differs? Does it differ because of SNV or indel, or because of different splicing? $\endgroup$
    – Shred
    Commented Sep 14, 2021 at 15:00
  • $\begingroup$ Just assume it could be any one or combination of those features. $\endgroup$
    – story
    Commented Sep 14, 2021 at 15:15

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In essence what you're looking for is targeted assembly. There aren't a lot of tools out there for that that I'm aware of, but on of them is Mapsembler. The general idea is to input a seed region and then let the program perform iterative extension of it. That sort of strategy should largely match your needs.

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  • $\begingroup$ Yeah this looks like exactly what I would be looking for! Will check it out and get back to you. $\endgroup$
    – story
    Commented Sep 14, 2021 at 16:29

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