[BioC] I need help making a dcf seed file to encapsulate a genome assembly im using.

Hervé Pagès hpages at fhcrc.org
Tue Jan 14 21:47:17 CET 2014

Hi Alan,

[I'm cc'ing the list so others can benefit from this.]

On 01/14/2014 08:13 AM, ashteyma at andrew.cmu.edu wrote:
> Hello,
>      I am working on a research project and I need to use a particular
> assembly of the yeast genome. I tried figuring out how to make a DCF
> file, But i was confused. I looked in the documentation but I'm
> confused about the correct way to make a dcf file from a text file.

You don't need to make a DCF file from a text file. A DCF file *is* a
text file. More precisely a DCF file is just a text file where the
content is organized as a collection of key/value pairs.

> If
> you have an example DCF file I could look at,

The BSgenomeForge vignette contains the full seed file that was used to
forge the BSgenome.Rnorvegicus.UCSC.rn4 package.
If you need more examples of seed files, the vignette also gives you a
list of more than 30 seed files that you can look at. All these seed
files are text files in the DCF format, that is, the information in
them is organized using the DCF syntax.

> some guaranteed method
> of making a seed file correctly, a video tutorial or anything that
> would help, can you please send it in response. Thank you.

No video tutorial sorry! The best way to make your own seed file is to
pick-up one of the seed files provided in the BSgenome package itself
(located in the extdata/GentlemanLab/ folder) and to modify it for your
own needs. In your case, the seed file for sacCer1, sacCer2, or sacCer3
should be close enough to what you need.

Finally note that the BSgenomeForge vignette in the devel version
of the BSgenome package has been reorganized to reflect the fact that,
starting with BioC 2.14, the BSgenome data packages don't contain
masks anymore (by default). As a consequence, the vignette is simpler
and probably a little bit easier to follow.

Hope this helps,

> Sincerely,
> Alan Shteyman
> Carnegie Mellon University

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

More information about the Bioconductor mailing list