LncRNA Nomenclature

Question

[jain72744]

I had RNA-seq data from which I extracted all lncRNAs by naming using BiomaRt package in R with ENST labels. Now I have another dataset with ENSG labels and if I convert it to ENST labels, I get repetitions of the data as for gene there are multiple transcripts. Is there a more appropriate way to do this or should I stick to ENSG IDs for lncRNAs.

Another query is that I have genbank accesion IDs for a dataset. IS it possible to convert it to ENST/ENSG data?

[ATpoint]

RNA-seq is typically analyzed on gene rather than transcript level. Are your counts gene or transcript?

[jain72744]

My data is based on gene counts and the respective gene IDs are given so I should work with ENSGs?

lncRNA_transcripts <- getBM(attributes = c("ensembl_transcript_id_version", "ensembl_gene_id_version", "external_gene_name"), filters = "biotype", values = "lncRNA", mart = ensembl)

I used this code to filter lncRNAs in my data.