Answers.Body: <p>If you have a SNP panel then you have the coordinates on the genome. You can use tools such as <a href="https://bedtools.readthedocs.io/en/latest/content/tools/slop.html" rel="nofollow noreferrer">bedtools slop</a> to expand the coordinates to the desired length and then extract those regions from the target genome using <a href="https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html" rel="nofollow noreferrer">bedtools getfasta</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-07-01T04:20:54.210Z
Answers.Text: Thank you! That's very helpful. The dilemma, however, is we'd like to extract the 300bp sequences from a different genome, and not from the reference genome of the SNP panel, therefore the coordinates on the SNP panel will not be exactly on our genome.
Answers.UserDisplayName: Umi Rayearth
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Answers.CreationDate: 2022-07-01T07:51:28.863Z
Answers.Text: Then you need liftover https://genome.ucsc.edu/cgi-bin/hgLiftOver
  I don't know if the genomes you're working on have mapping files though.
Answers.UserDisplayName: asafpr
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Answers.CreationDate: 2022-06-29T06:04:41.580Z
Answers.LastActivityDate: 2022-06-29T06:04:41.580Z
Answers.UserDisplayName: asafpr
Body: <p>I have about 300 90-bp sequences which I would like to map to a reference genome to make it longer to a 300bp sequence, wherein the 90bp is at the middle.</p>
  <p>Anyone knows what bioinformatics tool I can use for this? Thank you!</p>
  <p><em>Actual scenario:</em>
  The SNP sequences are from a SNP panel data (90bp sequence, SNP is at the middle). We would like to extend the sequence to 300bp, retaining the SNP at the middle so we can make a sequence capture panel of the SNP.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-29T06:38:19.690Z
Comments.Text: You mean the target capture panel of SNP markers?
Comments.UserDisplayName: envs_h_gang_5
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-29T12:41:43.580Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
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Comments.CreationDate: 2022-07-01T04:17:30.433Z
Comments.Text: @envs_h_gang_5 I'm actually not very familiar, but something like 'genotyping by sequencing' kind of panel.
Comments.UserDisplayName: Umi Rayearth
Tags: <phylogenetics><snp><read-mapping>
Title: What tool I can use to map short-reads sequences to reference genome and get specific mapped size
ThreadText: # What tool I can use to map short-reads sequences to reference genome and get specific mapped size
  
  (Asked by: username_0 on 2022-06-29)
  
  I have about 300 90-bp sequences which I would like to map to a reference genome to make it longer to a 300bp sequence, wherein the 90bp is at the middle.
  
  Anyone knows what bioinformatics tool I can use for this? Thank you!
  
  *Actual scenario:*
  The SNP sequences are from a SNP panel data (90bp sequence, SNP is at the middle). We would like to extend the sequence to 300bp, retaining the SNP at the middle so we can make a sequence capture panel of the SNP.
  
  **Tags:** phylogenetics, snp, read-mapping
  
  > **Comments:**
  > **username_1**: You mean the target capture panel of SNP markers?  
  > **username_2**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_0**: @username_1 I'm actually not very familiar, but something like 'genotyping by sequencing' kind of panel.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2022-06-29. Score: 3
  
  If you have a SNP panel then you have the coordinates on the genome. You can use tools such as [bedtools slop](https://bedtools.readthedocs.io/en/latest/content/tools/slop.html) to expand the coordinates to the desired length and then extract those regions from the target genome using [bedtools getfasta](https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html).
  
  > **Comments:**
  > **username_0**: Thank you! That's very helpful. The dilemma, however, is we'd like to extract the 300bp sequences from a different genome, and not from the reference genome of the SNP panel, therefore the coordinates on the SNP panel will not be exactly on our genome.  
  > **username_3**: Then you need liftover https://genome.ucsc.edu/cgi-bin/hgLiftOver I don't know if the genomes you're working on have mapping files though.  
  
  ---
  
  