Answers.Body: <p>As far as I'm aware, Illumina provide CSV annotation files for all their sequencing chips, which can be used when they can't be found in Bioconductor. You can find annotation information for the PorcineSNP60 <a href="https://support.illumina.com/downloads/porcinesnp60-v2_product_files.html" rel="noreferrer">here</a>, in particular the Manifest file (CSV format). The format is Illumina's weird "we say it's a CSV because there are commas in it" format, so if there are only a few locations of interest it would be easier to use grep than try to work out the right way to load it into R (or similar).</p>
  
  <p>For completeness, you want the lines between <code>[Assay]</code> and <code>[Controls]</code>. Here's an example way to pre-process the "CSV" file into a more standard format that just has one data table in it:</p>
  
  <pre><code>$ grep -n '^\[' PorcineSNP60v2_15031945_C1.csv 
  2:[Heading]
  7:[Assay]
  61574:[Controls]
  ### See that the table starts at line 8 (after [Assay]),
  ###   and finishes at line 61753
  $ tail -n +8 PorcineSNP60v2_15031945_C1.csv | head -n $((61574-8)) &gt; cleaned_PorcineSNP60v2_15031945_C1.csv
  </code></pre>
  
  <p>But for a few markers and grep, it doesn't matter if you're working with the clean or dirty CSV file:</p>
  
  <pre><code>$ grep -e '^IlmnID' -e '^MARC0073381' -e '^ALGA0066960' PorcineSNP60v2_15031945_C1.csv
  IlmnID,Name,IlmnStrand,SNP,AddressA_ID,AlleleA_ProbeSeq,AddressB_ID,AlleleB_ProbeSeq,GenomeBuild,Chr,MapInfo,Ploidy,Species,Source,SourceVersion,SourceStrand,SourceSeq,TopGenomicSeq,BeadSetID,Exp_Clusters,Intensity_Only
  ALGA0066960-2_B_F_2199219285,ALGA0066960,BOT,[T/G],0054749354,TGCCACAGGTCTGCTCAGCTCAAGCCCAACACTCGCAAGATACAGGTCTA,,,10.2,12,55218591,diploid,Sus scrofa,PorcineSNP60v2,2,BOT,GGCTCACCTCTGCCACAGGTCTGCTCAGCTCAAGCCCAACACTCGCAAGATACAGGTCTA[T/G]CCAGGCTTCTCTCTCCTACTCCTAGGGCCCCTGATGGTTCCTGCATCCTGACCAATAGTG,CACTATTGGTCAGGATGCAGGAACCATCAGGGGCCCTAGGAGTAGGAGAGAGAAGCCTGG[A/C]TAGACCTGTATCTTGCGAGTGTTGGGCTTGAGCTGAGCAGACCTGTGGCAGAGGTGAGCC,670,3,0
  MARC0073381-2_T_F_2199252059,MARC0073381,TOP,[A/G],0047761415,TGGAACGGATGGTGGAGACATTCTGGAGACAGAAGACAAACTGCTTCAGA,,,10.2,7,61808556,diploid,Sus scrofa,PorcineSNP60v2,2,TOP,CAACTGTGGTTGGAACGGATGGTGGAGACATTCTGGAGACAGAAGACAAACTGCTTCAGA[A/G]CAAAGCTCAGGAAGGCAA,CAACTGTGGTTGGAACGGATGGTGGAGACATTCTGGAGACAGAAGACAAACTGCTTCAGA[A/G]CAAAGCTCAGGAAGGCAA,660,3,0
  </code></pre>
  
  <p>I can see from this that the first marker is Chromosome 12, position 55218591, and the second marker is Chromosome 7, position 61808556. The Illumina annotation doesn't include the nearest gene, so you'll need to hunt for those locations on a genome browser (or using mapping with Bioconductor).</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-02-02T05:49:26.387Z
Answers.LastActivityDate: 2018-02-02T05:49:26.387Z
Answers.UserDisplayName: gringer
Body: <p>I have a couple of SNP identifiers such as MARC0073381 or ALGA0066960. The corresponding platform is Illumina Porcine SNP60 BeadChip (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL11379" rel="nofollow noreferrer">WG-410</a>).</p>
  
  <p>I want to know if these SNP are located within a promoter region of a gene.</p>
  
  <p>Bioconductor offers <a href="https://bioconductor.org/packages/release/data/annotation/html/porcine.db.html" rel="nofollow noreferrer">information</a> for Affymetrix chips, but I am not able to map the identifiers.</p>
  
  <p>How can I map SNPs from the beadchip to the porcine genome?</p>
  
Tags: <r><bioconductor><snp><illumina><porcine>
Title: SNP located within a promoter region (pig)
ThreadText: # SNP located within a promoter region (pig)
  
  (Asked by: username_0 on 2018-02-02)
  
  I have a couple of SNP identifiers such as MARC0073381 or ALGA0066960. The corresponding platform is Illumina Porcine SNP60 BeadChip ([WG-410](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL11379)).
  
  I want to know if these SNP are located within a promoter region of a gene.
  
  Bioconductor offers [information](https://bioconductor.org/packages/release/data/annotation/html/porcine.db.html) for Affymetrix chips, but I am not able to map the identifiers.
  
  How can I map SNPs from the beadchip to the porcine genome?
  
  **Tags:** r, bioconductor, snp, illumina, porcine
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-02-02. Score: 5
  
  As far as I'm aware, Illumina provide CSV annotation files for all their sequencing chips, which can be used when they can't be found in Bioconductor. You can find annotation information for the PorcineSNP60 [here](https://support.illumina.com/downloads/porcinesnp60-v2_product_files.html), in particular the Manifest file (CSV format). The format is Illumina's weird "we say it's a CSV because there are commas in it" format, so if there are only a few locations of interest it would be easier to use grep than try to work out the right way to load it into R (or similar).
  
  For completeness, you want the lines between `[Assay]` and `[Controls]`. Here's an example way to pre-process the "CSV" file into a more standard format that just has one data table in it:
  
  ```
  $ grep -n '^\[' PorcineSNP60v2_15031945_C1.csv 
  2:[Heading]
  7:[Assay]
  61574:[Controls]
  ### See that the table starts at line 8 (after [Assay]),
  ###   and finishes at line 61753
  $ tail -n +8 PorcineSNP60v2_15031945_C1.csv | head -n $((61574-8)) > cleaned_PorcineSNP60v2_15031945_C1.csv
  
  ```
  
  But for a few markers and grep, it doesn't matter if you're working with the clean or dirty CSV file:
  
  ```
  $ grep -e '^IlmnID' -e '^MARC0073381' -e '^ALGA0066960' PorcineSNP60v2_15031945_C1.csv
  IlmnID,Name,IlmnStrand,SNP,AddressA_ID,AlleleA_ProbeSeq,AddressB_ID,AlleleB_ProbeSeq,GenomeBuild,Chr,MapInfo,Ploidy,Species,Source,SourceVersion,SourceStrand,SourceSeq,TopGenomicSeq,BeadSetID,Exp_Clusters,Intensity_Only
  ALGA0066960-2_B_F_2199219285,ALGA0066960,BOT,[T/G],0054749354,TGCCACAGGTCTGCTCAGCTCAAGCCCAACACTCGCAAGATACAGGTCTA,,,10.2,12,55218591,diploid,Sus scrofa,PorcineSNP60v2,2,BOT,GGCTCACCTCTGCCACAGGTCTGCTCAGCTCAAGCCCAACACTCGCAAGATACAGGTCTA[T/G]CCAGGCTTCTCTCTCCTACTCCTAGGGCCCCTGATGGTTCCTGCATCCTGACCAATAGTG,CACTATTGGTCAGGATGCAGGAACCATCAGGGGCCCTAGGAGTAGGAGAGAGAAGCCTGG[A/C]TAGACCTGTATCTTGCGAGTGTTGGGCTTGAGCTGAGCAGACCTGTGGCAGAGGTGAGCC,670,3,0
  MARC0073381-2_T_F_2199252059,MARC0073381,TOP,[A/G],0047761415,TGGAACGGATGGTGGAGACATTCTGGAGACAGAAGACAAACTGCTTCAGA,,,10.2,7,61808556,diploid,Sus scrofa,PorcineSNP60v2,2,TOP,CAACTGTGGTTGGAACGGATGGTGGAGACATTCTGGAGACAGAAGACAAACTGCTTCAGA[A/G]CAAAGCTCAGGAAGGCAA,CAACTGTGGTTGGAACGGATGGTGGAGACATTCTGGAGACAGAAGACAAACTGCTTCAGA[A/G]CAAAGCTCAGGAAGGCAA,660,3,0
  
  ```
  
  I can see from this that the first marker is Chromosome 12, position 55218591, and the second marker is Chromosome 7, position 61808556. The Illumina annotation doesn't include the nearest gene, so you'll need to hunt for those locations on a genome browser (or using mapping with Bioconductor).
  
  
  ---
  
  