Hi everyone,
I have been using the biomart package to retrieve the exon sequences of certain genes. In particular I am only interested in the first exon of the gene which also includes the 5' UTR.
For this I have used the following code:
ID <- "ENST00000502732.6"
sequence <-getSequence(id = ID ,seqType = "gene_exon", type = "ensembl_transcript_id_version", mart = ensembl)
When I look at the resulting dataframe I obtain all the exon sequences. However, the exons are in the wrong order. Meaning that the sequence of exon1 is not necessarily in row 1 (and the rows are not labeled). Since I am particularly interested in exon 1, this is quite annoying as I would need to check the sequences manually again.
Am I missing something here?
Any help is appreciated. Also if there is another way to retrieve sequences of one particular exon it would be great to know.
Thanks in advance!
Thanks for your answer. Do I have to do it manually? Or can yo uthink of a different way? I have a list of 100 genes and doing it all manually might be quite labor intensive
Re-query, and this time, ask for exon rank, not just sequence.