I’m trying to run GOSeq on my data set of Arabidopsis thaliana transcripts. I have prepared the two input files for GoSeq as described in the hands on RNAseq tutorial, namely the Gene Ids and differential expression and the gene Ids and length files. The arabidopsis thaliana genome is not one of the available genomes in GoSeq so I downloaded the GO annotations from TAIR as a .txt.gz zipped folder. I extracted this and deleted headers and unwanted columns to just have the gene Ids and the GO terms as described in the GoSeq Help and saved as a tab delimited .txt file.
I can import this file into Galaxy and it looks as I would expect with the two columns. GoSeq allows me to select it from my history as the gene categories file but when I run GoSeq I get an error message- see below.
Any ideas what I am doing wrong?
