Thursday, June 14, 2012

Reformat 23andMe Data for SeattleSNP

Step #1: Download Raw Data from 23andMe

  • After signing into 23andMe, first go to "Account" (in the top right hand corner of the screen) and then "Browse Raw Data"
  • Click the link near the top of the page to "download raw data"
  • Choose "All DNA" for your data set, and then click "Download Data"

Step #2: Reformat Raw Data

  • Download the perl script 23andMe_to_SeattleSNP.pl
  • There is one parameter that you need to enter:
    • genome = raw data file from 23andMe
  • PC Users
    • Open a terminal window (type "cmd" in Run, for example)
    • Move to the folder where your 23andMe data is saved.
      • Basic commands:
        • cd = change folder
          • For example, If the data is in your D:\ drive, you can type "cd \d D:"
        • .. = move up one folder
    • Type in "perl 23andMe_to_SeattleSNP.pl" and enter the required genome parameter. See example below  (click to enlarge) .

  • Mac Users
    • Open Terminal (in Applications/Utilities, for example)
    • Basic commands:
      • cd = change folder
      • .. = move up one folder
    • Type in "perl 23andMe_to_SeattleSNP.pl" and enter the required genome parameter. See example below (click to enlarge).


Step #3: Upload Data to SeattleSNP

The 23andMe SNP data currently uses NCBI 36 / hg18.  You can confirm if this is still the case by using a text editor like Notepad++ to view the raw data.

There are a few different portals to access SeattleSNP annotations, but you will need to use this link if the 23andMe data is currently using NCBI 36 (as of today, NCBI 37 / hg19 is the latest genome build): http://snp.gs.washington.edu/SeattleSeqAnnotation/

  • Enter your e-mail address
  • Select the file created by the perl script.  It should be almost identical to the genome file, but it will say _SeattleSNP.txt at the end of the file
  • This file conforms to the "custom" format, so please select "custom" under "input file format" and enter the following information
    • Chromosome: 2
    • Location: 3
    • Reference Allele: 0
    • First Allele: 4
    • Second Allele: 5
  • Click the green submit button
  • It may take several hours to annotate your 23andME SNPs.  You will recieve an e-mail message when the annoted file is ready to download.
I have tested my perl scripts on a PC and Mac, but I cannot guarentee that they will work on every possible platform.   Also, these scripts may need modifications as file formats change, but I have currently confirmed that my scripts work with v2 and v3 arrays using genomes from Genomes Unzipped.  If you have any questions or comments, please post them below and I will do my best to help troubleshoot.

48 comments:

  1. This comment has been removed by a blog administrator.

    ReplyDelete
  2. Positive site, where did u come up with the information on this posting?I have read a few of the articles on your website now, and I really like your style. Thanks a million and please keep up the effective work. Data Blending in Tableau

    ReplyDelete
  3. This comment has been removed by the author.

    ReplyDelete
  4. This comment has been removed by a blog administrator.

    ReplyDelete
  5. I just got to this amazing site not long ago. I was actually captured with the piece of resources you have got here. Big thumbs up for making such wonderful blog page!
    Data Science Certification in Bangalore

    ReplyDelete
  6. I am really enjoying reading your well written articles. It looks like you spend a lot of effort and time on your blog.
    Data Science Course in Hyderabad | Data Science Training in Hyderabad

    ReplyDelete
  7. This comment has been removed by a blog administrator.

    ReplyDelete
  8. I really enjoy simply reading all of your weblogs. Simply wanted to inform you that you have people like me who appreciate your work. Definitely a great post. Hats off to you! The information that you have provided is very helpful.
    Data Science Course in Hyderabad

    ReplyDelete
  9. This comment has been removed by a blog administrator.

    ReplyDelete
  10. Actually I read it yesterday but I had some thoughts about it and today I wanted to read it again because it is very well written.

    ReplyDelete
  11. Thank you, Alex!

    It was written a while ago, so I was surprised about all the comments. Even though I would personally consider a lot of those spam, I kept them if they mentioned something that was even somewhat related. I didn't want readers to think I was censoring the comments too much (and I also left the note for anything that I thought needed to be removed for the same reason).

    ReplyDelete
  12. Very impressive and interesting blog found to be well written in a simple manner that everyone will understand and gain the enough knowledge from your blog being more informative is an added advantage for the users who are going through it. Once again nice blog keep it up.

    360DigiTMG Artificial Intelligence Course

    ReplyDelete
  13. This content is written very well. Your use of formatting when making your points makes your observations very clear and easy to understand. Thank you. blog comment

    ReplyDelete
  14. This comment has been removed by a blog administrator.

    ReplyDelete
  15. This comment has been removed by a blog administrator.

    ReplyDelete
  16. If you don't mind, then continue this excellent work and expect more from your great blog posts
    machine learning masters


    ReplyDelete
  17. Awesome article! I want people to know just how good this information is in your article. It’s interesting, compelling content. Your views are much like my own concerning this subject. seo services

    ReplyDelete
  18. This is a truly good site post. Not too many people would actually, the way you just did. I am really impressed that there is so much information about this subject that have been uncovered and you’ve done your best, with so much class. If wanted to know more about green smoke reviews, than by all means come in and check our stuff. seo backlinks

    ReplyDelete
  19. Hi, I find reading this article a joy. It is extremely helpful and interesting and very much looking forward to reading more of your work.. Posicionamiento WEB

    ReplyDelete
  20. Your work is truly appreciated round the clock and the globe. It is incredibly a comprehensive and helpful blog. domain rating

    ReplyDelete
  21. Really impressed! Everything is a very open and very clear clarification of the issues. It contains true facts. Your website is very valuable. Thanks for sharing.
    Data Science Course in Pune

    ReplyDelete
  22. Informative blog post,
    Google Adwords Certification Course the student will learn how to use PPC, CPC, CPM, CPA, Display Ads, Shopping Ad Campaign and he will also learn how to promote a website online.

    ReplyDelete
  23. Thanks a lot for sharing kind of information. Your article provides such great information with good knowledge. Digital Marketing Training in Pune

    ReplyDelete
  24. On your place I would make a video about it and get youtube likes from this site https://soclikes.com/

    ReplyDelete
  25. This is really very nice post you shared, i like the post, thanks for sharing..
    data science training

    ReplyDelete
  26. Very nice job... Thanks for sharing this amazing and educative blog post!
    data science training in malaysia

    ReplyDelete
  27. Very informative message! There is so much information here that can help any business start a successful social media campaign!

    Data Science Course in Nashik

    ReplyDelete
  28. Your site is truly cool and this is an extraordinary moving article.
    data science training in malaysia

    ReplyDelete
  29. 360DigiTMG is the most recommended Data Science course institute in Chennai. Get trained by top professionals from IIT, IIM and, ISB. Enroll now!

    Data Science in Bangalore

    ReplyDelete
  30. Are you not ready to risk your and your family's health this pandemic time by joining an offline Data Analyst course. we have a solution for you, enroll in an online Data Analyst course that will equip you with all the knowledge needed for a job in just 6 months.

    Data Analytics Course in Calicut

    ReplyDelete
  31. Data Science has specific deliverables and goals that include it. These deliverables assist in addressing the objectives of fixing the issue at hand.

    Data Science Training in Jodhpur

    ReplyDelete
  32. With decision making becoming more and more data-driven, learn the skills necessary to unveil patterns useful to make valuable decisions from the data collected. Also, get a chance to work with various datasets that are collected from various sources and discover the relationships between them. Ace all the skills and tools of Data Science and step into the world of opportunities with the Best Data Science training institutes in Bangalore.

    Data Science Course in Bangalore with Placement

    ReplyDelete
  33. 36DigiTMG offers top-rated courses in Data Analytics for your need and expertise. Get trained from industry experts with 170 plus hours of assignments that will help you bag a high-paying job.


    Best Data Science Training institute in Bangalore

    ReplyDelete
  34. Venture into the world of opportunities with Data Science in Bangalore and learn the valuable skills to demonstrate your capabilities to tackle this evolution of huge data. Avail benefits like Placement Assistance, Mock Interview, and Resume Building support from the placement team. Enroll now and learn Python, Tableau, SQL, Hadoop, and Spark to become a specialist in Data Science.

    Data Science in Bangalore

    ReplyDelete
  35. This comment has been removed by the author.

    ReplyDelete
  36. I am really enjoying reading your well written articles. It looks like you spend a lot of effort and time on your blog. I have bookmarked it and I am looking forward to reading new articles. Keep up the good work.
    data science course kanpur

    ReplyDelete
  37. This comment has been removed by the author.

    ReplyDelete
  38. This comment has been removed by the author.

    ReplyDelete
  39. This comment has been removed by the author.

    ReplyDelete
  40. Apart from ads, SaveFrom.Net also records users downloading behaviors as well as IP addresses. Personal data has a chance to leak while using the website.en.savefrom.net remove

    ReplyDelete

 
Creative Commons License
Charles Warden's Science Blog by Charles Warden is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 United States License.