Question: Viewing Non-Standard Genomes
2
gravatar for KCC
6.6 years ago by
KCC3.9k
Cambridge, MA
KCC3.9k wrote:

Is there a way to look at a non-standard genome in a genomics browser like IGV or IGB? I usually use IGV so that would be by preference for a genome browser, but given that I currently have no way of looking at my genome, I would settle for anything.

Basically, I know how many chromosomes by genome has and how big the chromosomes are. I just need something in which to view a wig file for my genome.

EDIT: Yes, I do have a fasta file of the genome.

Also, I don't care that much about the format: wig, bedgraph, bigwig, bigbedgraph. It's just that my data happens to be in wig so I guess i kind of wrote that without thinking. I know how to convert if I need to.

visualization • 2.1k views
ADD COMMENTlink modified 6.6 years ago by deanna.church1.1k • written 6.6 years ago by KCC3.9k

Can you provide a bit more information? Do you have a FASTA file for your genome? Is the genome submitted to GenBank/ENA/DDBJ?

ADD REPLYlink written 6.6 years ago by deanna.church1.1k
1

IGV will accept a new genome. Create a new .genome file using the menu option All you need is the fasta file. Also you can load annotation from local files (e.g. gff)

ADD REPLYlink written 6.6 years ago by Alastair Kerr5.2k
4
gravatar for Istvan Albert
6.6 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

This is just to expand on the comments by Alastair Kerr and deanna.church and combine them into an answer.

Every genome browser offers the option to import a custom genome. Usually located under names as such as "Import Genome". You just need a FASTA file that will then be indexed and saved in a format that the browser can load quickly. If your genome is large this may take a while to run.

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Istvan Albert ♦♦ 81k
2
gravatar for Zev.Kronenberg
6.6 years ago by
United States
Zev.Kronenberg11k wrote:

The web apollo team has a really impressive browser. It suports wig format. There is some overhead setting it up, but once that is done it is pretty smooth. Size shouldn't be a problem.

http://gmod.org/wiki/WebApollo

ADD COMMENTlink written 6.6 years ago by Zev.Kronenberg11k
1

Seconding the suggestion of WebApollo. It's built on the same framework as JBrowse (http://jbrowse.org; AJAX-y version of the popular genome browser GBrowse), it's very slick and fast, and is great for collaborative manual annotation of genomes. You can get WebApollo, JBrowse, GBrowse, plus other GMOD tools (Chado DB, Tripal DB interface) on GMOD in the Cloud, which is a virtual machine hosted in the Amazon cloud - everything is installed and ready to go; you just load your data. See http://gmod.org/wiki/Cloud for more on GMOD in the Cloud.

ADD REPLYlink written 6.6 years ago by girlwithglasses280
1
gravatar for deanna.church
6.6 years ago by
deanna.church1.1k
Bethesda, MD
deanna.church1.1k wrote:

NCBI also has a client side tool called genome workbench (http://www.ncbi.nlm.nih.gov/tools/gbench). If the assembly is in our Assembly DB (http://www.ncbi.nlm.nih.gov/assembly) you can just search and load it. If it is a private assembly, you can load FASTA files (or AGPs if they point to accession.versions). You can load annotation files as well as doing other analysis (alignments, etc).

ADD COMMENTlink written 6.6 years ago by deanna.church1.1k
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