Answers.Body: <p>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 <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-48" rel="nofollow noreferrer">Mapsembler</a>. 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.</p>
  
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Answers.CreationDate: 2021-09-14T16:29:30.727Z
Answers.Text: Yeah this looks like exactly what I would be looking for! Will check it out and get back to you.
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Answers.CreationDate: 2021-09-14T16:21:38.407Z
Answers.LastActivityDate: 2021-09-14T16:21:38.407Z
Answers.UserDisplayName: Devon Ryan
Body: <p>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.</p>
  <p>Is there a way for me to do a &quot;transcriptome assembly&quot; with a specific read or sequence as a starting point? And only do the k-mer assembly from that single sequence?</p>
  <p>I could probably code something myself but I feel like a tool to do this must already exist?</p>
  <p>The goal here is to avoid the significant overhead of assembling a whole transcriptome when I'm only interested in one gene.</p>
  <p>NOTE: In this case the data is RNA-seq</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-09-14T15:00:52.317Z
Comments.Text: What did you mean by *genome sequence differs*? Does it differ because of SNV or indel, or because of different splicing?
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Comments.CreationDate: 2021-09-14T15:15:17.107Z
Comments.Text: Just assume it could be any one or combination of those features.
Comments.UserDisplayName: story
Tags: <rna-seq><assembly><k-mer><stringtie><trinity>
Title: Assembling all transcripts for an individual gene? (using single sequence to seed the assembly)
ThreadText: # Assembling all transcripts for an individual gene? (using single sequence to seed the assembly)
  
  (Asked by: username_0 on 2021-09-14)
  
  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
  
  **Tags:** rna-seq, assembly, k-mer, stringtie, trinity
  
  > **Comments:**
  > **username_1**: What did you mean by *genome sequence differs*? Does it differ because of SNV or indel, or because of different splicing?  
  > **username_0**: Just assume it could be any one or combination of those features.  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2021-09-14. Score: 1
  
  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](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-48). 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.
  
  > **Comments:**
  > **username_0**: Yeah this looks like exactly what I would be looking for! Will check it out and get back to you.  
  
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