Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2.5
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Sprint:Summer 7
Description
A lot of people who use genome sequencing services communicate using social media platforms. We need to know what people are saying about the services, how they use the data, and why they want to get their genomes sequenced.
Let's investigate a social media platform in this ticket and find out what people are saying or asking about individual genome sequencing services.
Facebook and Reddit are platforms where users can create long discussion threads, so let's start with them.
Facebook requires login and people tend to use private groups, indicating they don't really want their comments to become widely read or known. So, let's not use Facebook, out of respect for people's privacy.
Reddit, however, is more or less completely public. Users on reddit are expecting and even hoping that sometimes their posts will be shared and even commented on outside the Reddit user community. For example, there are "subreddits" that are semi-humorous or semi-serious, like the "am the .[fill in insult]. " subreddit where people describe awkward social situations and ask whether they did the right thing, or not. Also, it seems like people from the companies themselves participate and try to answer questions.
Let's find and summarize links to public posts on Reddit where people discuss genome sequencing services - what they like, what they don't like, questions they may have about the platforms, or other topics. Add links, quotations from conversations, and your thoughts and commentary as individual comments below.
To complete this task, present your results to the team. Summarize using a slide deck or other format as you see fit. The goal is to make sure that everybody on the team will understand what are saying about individual genome sequencing on social media.
Big questions we have:
- How can our genome browser software help people understand human genome sequence data?
- Are people using genome browsers to look at their data. If yes, which ones?
- Are people misunderstanding what their data are, or do they seem to have a pretty good idea of what the data mean?
- What types of training materials could we create that would help people learn to use Integrated Genome Browser to explore human genome sequencing data? What "how-to" guides do reddit users like or link to?
Attachments
Issue Links
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Activity
I looked for posts within the past year or two and found quite a few! Some mention sequencing company options while others talk about tools that can be used to analyze raw sequencing data. I'll summarize and link to each post below:
- Companies that offer direct-to-consumer whole exome sequencing - This user wanted to generate WES/WGS data for a friend's family that may have a possible inherited neurological disorder. Although there are a number of companies that offer direct-to-consumer WES, like Helix and 23&me, you can’t download the data or they make it prohibitively expensive. Nebula Genomics and Dante Labs were recommended most often, but Veritas Genetics, Gene By Gene, Sequencing.com, Macromo, and seqcenter were also mentioned as options for this user.
- Whole Genome Sequence - This user wants to have their genome sequenced so that they can use it as a reference dataset of some kind. They want the data in the most commonly-used file format (whatever that may be) so that this data can be re-analyzed in the future. They also want a company that doesn't use a subscription model so that they don't have to pay for the data forever. Nebula Genomics was the most recommended, but Dante Labs, Genomes.io, and PolyCypher were also mentioned as options.
- Got my genome sequenced. Is there a free tool I can use to analyze parts of the raw data? - They're looking for a tool that could take raw sequencing data and convert it to a 23&me-like format. There were lots of recommendations, including documentation created by a Reddit user that walks through how they annotated variants (https://joemcgirr.github.io/files/code_tutorials/my_genome/SnpEFF.html; https://joemcgirr.github.io/files/code_tutorials/my_genome/gwascat.html). Other recommendations include usegalaxy, Promethease, Genetic Genie's GenVue Discovery tool, YSeq, WGS Extract, and common command like tools like BWA and samtools.
- Whole Genome Sequencing Differences? - This user is asking about the differences between Nebula Genomics and Sequencing.com. One user suggests that Sequencing.com outsources their testing to Nebula so there should be no real quality differences between the two. There were other options suggested as well, like Dante Labs, Fullgenomes.com, Prevention Genetics Health screen, and YSeq. Dante Labs appears to include more relevant tests as well as an hour genetic consultation.
- My experience with sequencing.com - "Difficult to import ancestry.com DNA; I'm taken here: https://sequencing.com/welcome/how-to-access-download-use-ancestrydna-data When I attempt to import data using the link I found before registering (see data upload), I am told an email address will be sent to me from Ancestry and that I need to forward it to data@sequencing.com; however, no email arrives. Still have not imported my DNA. Two of the free genealogy apps of interest to me do not seem to be available. In short, maybe it will be worth it, but I'm beginning to have my doubts. They may claim "privacy forever" while allowing third-party apps to access DNA data with each third-party having its own privacy policy? It isn't clear. I did this for genealogy purposes; I am looking for any and all tools to aid my research and the apps look interesting, if they are available."
Here's another thread I forgot to include:
Does anyone know how to convert Nebula's DNA files (CRAM, CRAI, FASTQ, VCF, TBI), into the raw DNA data file almost all other companies use? - This user wants to know how to convert any of the six file types provided by Nebula (CRAM/CRAI, FASTQ, VCF, TBI) to RAW format which seems to be used by other companies. They didn't know, as consumers, that "raw" was referring to those fastq files!
This is great - thank you Paige Kulzer!
For the next steps, Nowlan Freese should read and review. And maybe add more threads, as well?
A suggestion: Let's come back to this page, re-read the threads, and develop a tutorial for the audience of questioners (OPs) and commenters, explaining how to open and view one's personal genome sequence data.
Request for Nowlan Freese : after you have reviewed and read the threads (and maybe added a few more) please close the ticket.
I looked through the various threads, I think this ticket is a good resource. I'm going to close it for now, but will be taking an additional look at the ticket next week as I work on IGBF-3854.
This thread:
Which company to choose for whole genome sequencing in 2024?
One poster in the above thread wrote: "AFAIK all these services are required to give you your raw data but it is good to check." AFAIK = "As far as I know" This is probably not correct. Who would require this? I think it is probably completely up to the company as to what types of data or services they provide. Am I wrong?
Another poster: "The sequencing is done in a CLIA certified lab." What is a "CLIA certified lab" for genome sequencing services?
(Added a nerdy-sounding post about IGB having a visualization feature for CRAM files soon, as user name u/Ashamed_Umpire4376. I did not pick that user name - the platform picked it for me LOL!)
Companies mentioned:
and others?