[BioC] How to get sequences corresponding to a GRanges?

Cei Abreu-Goodger cei at langebio.cinvestav.mx
Mon Oct 29 00:28:10 CET 2012

Hello all,

I was wondering if there was a simple way to get the sequences 
corresponding to the ranges stored in a GRanges object. If you have the 
original sequences in a BSgenome object, you can use 'getSeq'. But what 
if you just have the fasta file, imported as a DNAStringSet object?

I want to avoid having to forge a new BSgenome object each time, since 
I'm dealing with unfinished assemblies, with thousands of sequences that 
I don't want to split into individual fasta files, etc.

Many thanks,


Dr. Cei Abreu-Goodger
Profesor Investigador
Tel: (52) 462 166 3006
cei at langebio.cinvestav.mx

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