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?

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.