Answers.Body: <p>Numbers, usually in the form of 0/1/2, is a common way many formats represent bases.</p>
  <p>For example, if a SNPs has bases which are A/T, then these are encoded as 0/1, with the reference allele/base taking the 0 and the alternate allele/base taking 1.</p>
  <p>However, if you read <a href="https://rajanil.github.io/fastStructure/" rel="nofollow noreferrer">the documentation</a>, it says:</p>
  <blockquote>
  <p>Specifically, rows in the data file correspond to samples, with two
  rows per sample (note that only diploids are handled by this
  software), and columns correspond to SNPs. The first 6 columns of the
  file will be ignored; these typically would include IDs, metadata,
  etc. This software only handles bi-allelic loci. <strong>The two alleles at
  each locus can be encoded as desired</strong>; however, missing data should be
  encoded as `-9'.</p>
  </blockquote>
  <p>So you should be able to use your base letters here and it will work OK as long as the columns and rows are formatted correctly.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-09-23T12:52:07.487Z
Answers.LastActivityDate: 2020-09-23T12:52:07.487Z
Answers.UserDisplayName: user438383
Body: <p>The structure file for fastSTRUCTURE seem to be a table with rows and columns but the cells are all numbers, while my genotypes are simply bases. How could I know what I should insert there?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-23T12:22:15.270Z
Comments.Text: What format are your genotypes in at the moment? There is likely some tool someone has written to convert it to the correct format.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-23T12:40:03.460Z
Comments.Text: Just table of 'A/C' bases
Comments.UserDisplayName: hiddenhospitalresearch
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-23T12:41:53.800Z
Comments.Text: 'Table' isn't a format. What are the rows? What are the columns? Is it genotypes or alleles - i.e. is there one or two rows per marker? the more info you give, the easier it will be for someone to help you. Could you add a sample of your genotype format to the main answer so others can see it.
Comments.UserDisplayName: user438383
Tags: <file-formats>
Title: What should be the numbers in the fastSTRUCTURE file?
ThreadText: # What should be the numbers in the fastSTRUCTURE file?
  
  (Asked by: username_0 on 2020-09-23)
  
  The structure file for fastSTRUCTURE seem to be a table with rows and columns but the cells are all numbers, while my genotypes are simply bases. How could I know what I should insert there?
  
  **Tags:** file-formats
  
  > **Comments:**
  > **username_1**: What format are your genotypes in at the moment? There is likely some tool someone has written to convert it to the correct format.  
  > **username_0**: Just table of 'A/C' bases  
  > **username_1**: 'Table' isn't a format. What are the rows? What are the columns? Is it genotypes or alleles - i.e. is there one or two rows per marker? the more info you give, the easier it will be for someone to help you. Could you add a sample of your genotype format to the main answer so others can see it.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-09-23. Score: 4 | Accepted answer
  
  Numbers, usually in the form of 0/1/2, is a common way many formats represent bases.
  
  For example, if a SNPs has bases which are A/T, then these are encoded as 0/1, with the reference allele/base taking the 0 and the alternate allele/base taking 1.
  
  However, if you read [the documentation](https://rajanil.github.io/fastStructure/), it says:
  
  > Specifically, rows in the data file correspond to samples, with two
  > rows per sample (note that only diploids are handled by this
  > software), and columns correspond to SNPs. The first 6 columns of the
  > file will be ignored; these typically would include IDs, metadata,
  > etc. This software only handles bi-allelic loci. **The two alleles at
  > each locus can be encoded as desired**; however, missing data should be
  > encoded as `-9'.
  
  So you should be able to use your base letters here and it will work OK as long as the columns and rows are formatted correctly.
  
  
  ---
  
  