No Reference GFF file available in ClosestBed tool

bedtools
reference-annotation
#1

Hi,

I was trying to match my ChIP-seq peaks with nearest genes, for what I thought I’d use the ClosestBed tool. However there are no built-in GFF files available. Could you please add one for mouse?

Many thanks!

1 Like
#2

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):

#3

Thanks for your reply. I have downloaded one from iGenomes (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/Ensembl/GRCm38/Mus_musculus_Ensembl_GRCm38.tar.gz) and tried to launch the tool. I’m getting an error:
Fatal error: Exit code 1 ()
Error: Unable to determine type for file /galaxy-repl/main/files/030/235/dataset_30235478.dat

(The file name doesn’t correspond to the name of the genome file, but it must be it since my peak bed file is fine).

Could you please suggest what to do with that?
Many thanks

1 Like
#4

iGenomes: The entire “tar.gz” archive should not be uploaded to Galaxy. Just the genes.gtf dataset included in it. Also, it looks like you picked the Ensembl version of the mouse genome. The genome/build must match the genome/build that you originally mapped against. At Galaxy Main, this would be UCSC’s mm9 (GRCm37) or mm10 (GRCm38).

If the correct annotation is not picked, other problems can come up: FAQ

Gencode: The gtf data can be directly imported with Upload but will need some formatting standardization after. The data here is formatted with UCSC genome build identifiers. The most current release will be mm10 (GRCm38) and the prior release is mm9 (GRCm37).

Both will work, with Gencode sometimes easier for people to get (does not involve downloading, uncompressing, etc locally on your own computer).