Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.
This week’s highlighted question was from someone with personal genomics data in their hands, but doesn’t know what to do next.
I used 23andMe to download my raw genome. I have it in a .txt file but you can’t use the format for real bio programs. i want to make my own library for further analysis. Does anyone know how i can convert .TXT to FASTA, GenBank, or any other usable file type?
Although Biostar usually hosts questions from folks who are a bit more advanced in their grasp of file formats, this question struck me as interesting for a couple of reasons. The needs of folks who are not practitioners, but who find themselves with data in their hands, will only increase going forward. And although the companies will offer some tools, there’s a niche for some lighter-weight public tools. I discussed this before on the issue of genome browsers, which are currently too much heavy lifting for intro-level users. I know there are some open data communities forming around this data too, but so far what I’ve seen has been more sophisticated early adopter types.
But I imagine it would be difficult to get funding for such intro-level tools. They probably wouldn’t score well on “innovation” and some of the other traditional grant criteria because–well, because that’s not what the system does.
Maybe it would make some good class projects for some coders who are learning to build tools, and to work with this type of data. Make some gentle 23andme to X-format converters. A browser that’s not too hard to load your data up and look around without too many tracks. These folks are going to need more hand-holding. They don’t know what formats they need, or what is available for them to do.
But have a look at the answers, and if you have other guidance for this newbie, drop some comments over there.