Hi everyone,
I know that it sounds trivial, but I have been looking around (e.g. UCSC) for the mouse mm9 gene annotation file, and I can't get a clear fie with gene ID and genomic locations. I keep getting raw sequence files, alignment files,...
For example, with the Broad's IGV, you can put a gene name for mm9, and you the exact gene location. Hence, does anyone know how to get such file (e.g. from the Broad)? Or do I have to somehow build it myself?
Thank you.
3 answers
There are various resources, for example see this post Download gene names and annotations *.gff
Also look for similar posts in the right sidebar
From biomart you can download all annotations for mm9 or other builds or versions. Here is the link for from where you can download for all genes or for your genes of interests have a look at filters for your genes.
•
written
by
Ming Tommy Tang
Log in to answer this question.
-
Finding assembled transcript sequences from StringTie output
written by Jen •
-
The same location shares different GeneBank Accession in IGV and UCSC?
written by Andrew Liu •
-
Somatic mutations per gene
written by zephyr_falcon
-
How to find the promotor region of a given gene by using IGV
written by iibrams07 •
-
Batch query reference nucleotide
written by jennagu •
-
IGV command line control
written by damian.loska •
-
HOWTO get alternative splicing event for a specific gene
written by Assa Yeroslaviz
-
IGV and Variant Call
written by a_biologist •
-
How can I find the location of promoter of a gene?
written by karthik •
-
How to identify human samples with a specific mouse gene expression signature?
written by Avro
