Body: <p>We have some RNA from knock-in mice, there are two different sequences we're looking for. We have aligned to the mouse genome using STAR but the sequence isn't there which isn't too surprising What is the best way to check for the presence of the sequence? Should I just turn them into a sequence and use them as the reference genome for STAR to align to? Is there a way I can easily incorporate it into the existing genome so I could get read counts for everyhting including those reads? Should I just BLAST using something like magicblast?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-05T12:25:55.850Z
Comments.Text: Depends on the throughput. High throughput download the mouse genome and use Blat (a bit out of date now)? Megablast just make sure you select the mouse genome to speed the blasting.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-06T15:33:32.853Z
Comments.Text: @ATpoint could you give me some suggestions on what to search by any change? I couldn't really find anything useful partly because it kept talking about Indels.
Comments.UserDisplayName: Sethzard
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-06T15:34:21.783Z
Comments.Text: @Michael I'll look into that. Thanks.
Comments.UserDisplayName: Sethzard
Tags: <rna-seq><phylogenetics><rna-alignment>
Title: Best way to align to find inserted sequence
ThreadText: # Best way to align to find inserted sequence
  
  (Asked by: username_0 on 2020-11-05)
  
  We have some RNA from knock-in mice, there are two different sequences we're looking for. We have aligned to the mouse genome using STAR but the sequence isn't there which isn't too surprising What is the best way to check for the presence of the sequence? Should I just turn them into a sequence and use them as the reference genome for STAR to align to? Is there a way I can easily incorporate it into the existing genome so I could get read counts for everyhting including those reads? Should I just BLAST using something like magicblast?
  
  **Tags:** rna-seq, phylogenetics, rna-alignment
  
  > **Comments:**
  > **username_1**: Depends on the throughput. High throughput download the mouse genome and use Blat (a bit out of date now)? Megablast just make sure you select the mouse genome to speed the blasting.  
  > **username_0**: @ATpoint could you give me some suggestions on what to search by any change? I couldn't really find anything useful partly because it kept talking about Indels.  
  > **username_0**: @Michael I'll look into that. Thanks.  
  
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  ## 0 answers
  
  