I am trying to download information from JGI phytozome for a differential expression analysis I ran using DESeq2. A wealth of googling hasn't yielded anything that fixes the issue.
I'm trying to troubleshoot what I'm doing wrong so I have some test code below:
vol = useMart(biomart = "phytozome_mart", host="phytozome.jgi.doe.gov", dataset = "phytozome") IDS = c("Cre01.g000017.t1.1","Cre01.g000033.t1.1","Cre01.g000650.t1.1") check = getBM(attributes=c("transcript_name1","gene_name"), filters = "transcript_name_filter", values = IDS, mart = phytozome_mart)
Running this gives me a consistent error of:
Error in curl::curl_fetch_memory(url, handle = handle) : Could not resolve host: NA
Which I'm not sure how to resolve. I can successfully use listAttributes and listMarts on vol to see the information from phytozome, but I don't know why I get an error when trying to access them.
Any help would be appreciated. I've used biomaRt successfully in the past to pull information from other marts, so I'm not sure what's going wrong this time...