No Reference GFF file available in ClosestBed tool

[jennaj]

Hi,

At least for the near term, there will be no built-in reference annotation added to this tool. Instead, locate and upload a annotation source and use it “from the history”.

Mouse GTFs can be obtained from Gencode and iGenomes. These versions of the annotation will have the most utility across tools.

This prior Q&A is about human (hg38 + hg19) but the same sources/formatting advice applies for mouse (mm10 + mm9):

@jennaj

• For Gencode , copy the link to the GTF and paste it into the Upload tool: https://www.gencodegenes.org/. After it is loaded, remove the headers (lines that start with a “#”) with the Select tool using the options “NOT Matching” with the regular expression ^# . Once the formatting is fixed, change the datatype to be gft under Edit Attributes (pencil icon). The data will be given the datatype gff by default, which works fine with some tools and but not with others. Avoid the gff3 version of this particular data (contains duplicated IDs and several RNA-seq tools do not work with annotation in that format anyway).
• For iGenomes , the archive corresponding to the target genome/build needs to be locally downloaded, the tar archive unpacked, and then just the genes.gtf data uploaded to Galaxy (browse the local file, or use FTP). Find all available genome/builds here: iGenomes