Dear all,

 

I have a list of ensemble gene IDs and I need to get corresponding
sequences together with 5' upstream (4000 bp), 3'downstream (4000 bp)
and all introns.

I know that I probably can do this using a combination of commands:

 

Tmp1<-getSequence(id=
"ENSG00000128714",type="ensembl_gene_id",seqType="coding_gene_flank",ups
tream=4000,mart=human)

Tmp2<-getSequence(id=
"ENSG00000128714",type="ensembl_gene_id",seqType="coding_gene_flank",dow
nstream=4000,mart=human)

Tmp3<- getSequence(id=
"ENSG00000128714",type="ensembl_gene_id",seqType="cdna", mart=human)

 

and then concatenate tmp1, tmp2, tmp3, but I am not sure that 'cdna'
seqType will give me introns...

Also, I hope that there is a simpler way to get all these sequences
using just one command with the right 'seqType' specification.

 

Could someone please clarify this for me?

Thank you!

 

Best regards

Galina


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