How can I get Ensembl CDS / 3'UTR and 5'UTR sequences

Question

[2405592M]

Hi all,

I've finished doing an RNA-seq analysis and I've done some differential expression on my data set. I now want to do some codon usage analysis between conditions for my up and down regulated genes. How can one get the 3'UTR / CDS / 5'UTR sequences with ensembl IDs?

Thanks in advance!

Answer 1

[Emily]

BioMart! Filter by your list of Ensembl IDs and get the sequences as Attributes. There's a help video to get you started if you've never used BioMart before.

[2405592M]

Hi Emily,

I'm trying to do this through R using the following:

library(biomaRt)
listMarts()

ensembl <- useMart("ensembl")

datasets <- listDatasets(ensembl)
head(datasets)

ensembl = useDataset("mmusculus_gene_ensembl", mart = ensembl)

attributeNames_codon_usage <- c("ensembl_gene_id", "5utr", "coding", "3utr")

ourFilterType <- "ensembl_gene_id"

filterValues <- rownames(Day4_CONvsCRE)

codon_usage_mm10_annot_Day4_CONvsCRE <- getBM(attributes = attributeNames_codon_usage,
                                              filters = ourFilterType,
                                              values = filterValues,
                                              mart = ensembl)

but I keep getting the following error:

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 4 elements

[Emily]

You can't select multiple sequence types in one query, you would need to run them as three queries.

I would also recommend getting the transcript ID in your attributes, as you'll get a sequence for each one.