Question: I need help making a dcf seed file to encapsulate a genome assembly im using.
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gravatar for Hervé Pagès
5.7 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:
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, H. > > 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
cancer yeast bsgenome • 817 views
ADD COMMENTlink modified 5.7 years ago by ashteyma@andrew.cmu.edu10 • written 5.7 years ago by Hervé Pagès ♦♦ 14k
Answer: I need help making a dcf seed file to encapsulate a genome assembly im using.
0
gravatar for ashteyma@andrew.cmu.edu
5.7 years ago by
To Herve, Thank you, that helped. I tried searching in window explorer for a dcf file, but couldnt find anything i looked for the folder you mentioned and found it and i see an example now. It should be easy to modify it. thank you for the help. Sincerely, Alan > 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, > H. > > >> >> 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 >
ADD COMMENTlink written 5.7 years ago by ashteyma@andrew.cmu.edu10
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