Hi there
I've a total of 8000 list of genomic coordinates from mouse that I want to convert to gene names, is there a software out there that can do it quickly rather than I doing them manually from mouse phenome databases
thanks
Basically what you are wanting to perform is an annotation.
There are several ways to go about this, using annotation software. Have a look at the program R - the GenomicRanges and the BiomaRt packages will help you.
You should try ANNOVAR : http://annovar.openbioinformatics.org/en/latest/
Annovar is a program for annotating genetic variants, which may not be what the poster is asking for.
If you have a mutation list in VCF format, then annovar will be fine. However if you have genomic coordinates with no mutation information, and you want to map them to gene names, the packages in R that I mentioned above will help.
If you don't want to install R you can use BEDTools with intersectbed between one bed with your coordinate and one bed or gff with all genes in mouse (from ucsc or bed).
have a look to the public Galaxy server, you will find several tools for annotation.
Best
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics