I am analyzing bulk ATAC-seq for mouse samples. The tutorial of " ATAC-Seq data analysis" mentioned “Obtain Annotation for hg38 genes”. I want to know what is the best source is to obtain the annotation file for mouse genome
Welcome, @Na_Wang
You can get the annotation from UCSC or Gencode for the mouse genome. Make sure the data is from the exact same genomic assembly release as the fasta index you are using in Galaxy. The mouse indexes that are “built-in” were sourced from UCSC.
- UCSC Genome Browser Downloads
- https://www.gencodegenes.org
- FAQ: Working with GFF GFT GTF2 GFF3 reference annotation
And this is about the human genomes, but much of the information will apply to mouse genomes as well e.g. how to pay attention to and double check that your reference data is all a “match” from the same release.
And, an FAQ that may be helpful even though you are using slightly different tools. The core advice about how to ensure your data is formatted in a way that tools can understand will apply for most protocols.
Hope this helps or that you already solved this! 