[Bioc-sig-seq] Refseq vs Ensembl

kirti prakash kirtiprakash3.14 at gmail.com
Fri Nov 19 08:49:09 CET 2010


I am not sure if this is the right place to ask but here is my question.

When I take trancription start positions from the site below the total
tss count is around 37000.

When I query at ensembl the total tss count is around 137000.
mart <- useMart( "ensembl", dataset = "hsapiens_gene_ensembl" )
tss <- getBM( attributes=c( "transcript_start", "transcript_end",
"strand" ), filters="chromosome_name", values=c(1:23), mart=mart )

So is this the set of TSSs that includes alternative versions of genes
or I am missing something ?

Thank you,

Best regards,

Kirti Prakash

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