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Question: How do I create BSgenome Bos_taurus_UMD3.1?
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gravatar for mbk0asis
3.5 years ago by
mbk0asis0
Korea, Republic Of
mbk0asis0 wrote:

Hi.

I have been trying to create BSgenome for Bos_taurus_UMD_3.1.1 over a week but haven't succeeded.

I keep the error message below.

> library(BSgenome)
> forgeBSgenomeDataPkg("/PATH/TO/genome.fa")
Error: Line starting '>1 ...' is malformed!

 

I am really frustrated now because I'm not fluent in both English and R language.

Can somebody explain what is the problem and/or how to create a custom BSgenome step by step?

 

 

ADD COMMENTlink modified 3.5 years ago by Hervé Pagès ♦♦ 13k • written 3.5 years ago by mbk0asis0
2
gravatar for Hervé Pagès
3.5 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

Of course you cannot call forgeBSgenomeDataPkg() directly on a 2bit or FASTA file. You need to prepare a seed file first and then call forgeBSgenomeDataPkg() on the seed file. All this is explained in the BSgenomeForge vignette. Please see the thread you started on the bioc-devel mailing list for the follow-up on this:

https://stat.ethz.ch/pipermail/bioc-devel/2015-March/007223.html

Thanks,

H.

ADD COMMENTlink written 3.5 years ago by Hervé Pagès ♦♦ 13k
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