Question: Trying to visualize .bed file
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gravatar for brunobsouzaa
4.6 years ago by
brunobsouzaa490
Brazil
brunobsouzaa490 wrote:

I have some SNP data in .bed format... I'm trying to visualize this data to see the genotype of my patients... I've tried to use Plink 1.9 to look for those informations but couldn't do it! Can someone help me with this?!

snp • 2.4k views
ADD COMMENTlink modified 4.6 years ago by ablanchetcohen1.2k • written 4.6 years ago by brunobsouzaa490

How do you mean visualize? Which result do you aim to obtain? How many variants are included?

ADD REPLYlink written 4.6 years ago by WouterDeCoster45k
0
gravatar for Denise CS
4.6 years ago by
Denise CS5.1k
UK, Hinxton, EMBL-EBI
Denise CS5.1k wrote:

If you want to visualise your data, which is in bed file format, you may want to try attaching it to Ensembl. Check the Use my own data in Ensembl tutorial for a how-to. You can then compare your SNP data to the annotation of genes and variants (including structural variants from the 1000 genomes and DECIPHER) available in Ensembl. Make sure you know which coordinates your data in on, GRCh38 or GRCh37 (=hg19).

ADD COMMENTlink written 4.6 years ago by Denise CS5.1k
0
gravatar for ablanchetcohen
4.6 years ago by
ablanchetcohen1.2k
Canada
ablanchetcohen1.2k wrote:

Just use IGV. https://www.broadinstitute.org/igv/ IGV is, in my opinion, the best browser for viewing alignment files on your local computer.

You can also use the UCSC Genome Browser or Ensembl, as Denise suggested. The main advantage of using an online browser is that you'll have an easier access to more tracks from other data sources. The main disadvantage is that you have to upload your data, which is a problem if your files are large and you don't have access to a web server.

If you're experiencing problems with the size of your BED file, you'll first have to convert it to the bedgraph format and then to the bigWig format.

ADD COMMENTlink written 4.6 years ago by ablanchetcohen1.2k

It's a pity that one needs to register to IGV and download the application. Neither UCSC nor Ensembl need registration. Once you upload/attach your data to IGV (after creating an account), can you share the data you attached as a URL link from IGV?

ADD REPLYlink written 4.6 years ago by Denise CS5.1k
0
gravatar for ablanchetcohen
4.6 years ago by
ablanchetcohen1.2k
Canada
ablanchetcohen1.2k wrote:

The registration is annoying, but it really just takes a few seconds. The software is from the Broad Institute, so it's all open source. I guess the registration is just for them to keep track of the users, and justify their financing.

I didn't want to make my first post too long, but yes, that is the second disadvantage of a desktop browser like IGV versus an online one, like the Ensembl or the UCSC Genome Browser. You can't easily share links via a URL with IGV, while it is trivial with the UCSC Genome Browser (and probably the Ensembl Browser, which I don't normally use).

EDIT. Sorry, I keep making the mistake of posting a new answer, instead of answering a comment. There is no delete option to correct my mistake.

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by ablanchetcohen1.2k

Yes, you can share your attached data with Ensembl too and no need for registration (although you can register, and if you do there are perks for you). It's indeed annoying to have to register to access IGV. It took me forever to find out I had to register. I was just hoping to get to a browser view. Anyway, forums like Biostars are great as different people will have different ways to do things (e.g. attach own data) and it's important for users to know the diversity out there so that they have the chance to try and see what suit their needs best.

ADD REPLYlink written 4.6 years ago by Denise CS5.1k
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