[BioC] help with forging a BSgenome data

Hervé Pagès hpages at fhcrc.org
Tue Oct 8 08:54:38 CEST 2013

Hi Adeolu,

On 10/07/2013 03:32 AM, ADEWOYE, Adeolu B. (Dr.) wrote:
> Dear Herve,
> I am just wondering if it possible to forge a BSgenome data package from bam files?
> I have a very large bam files (140GB) I would like to forge into BSgenome data.
> Your advice on this would be greatly appreciated.

My understanding is that BAM files usually contain data (aligned
reads) of a slightly different nature than what usually goes into a
BSgenome data package (full genome sequences). I also heard that BAM
files are sometimes used to store genome assemblies but I've actually
never seen this kind of file. What do you have in your BAM files?
How were they generated?


> Many thanks,
> Adeolu
> Dr. Adeolu Adewoye
> University of Leicester
> Department of Genetics
> University Road
> Leicester
> UK

Hervé Pagès

Program in Computational Biology
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