Hello,
I am trying to plot genome coverage over the Arabidopsis thaliana genome using "karyoploteR". I tried to use BSgenome package to get the genome. The BSgenome package has TAIR9 genome which is old ( "BSgenome.Athaliana.TAIR.TAIR9"). I found that TAIR10.1 is available at https://bioconductor.statistik.tu-dortmund.de/packages/3.12/data/annotation/html/BSgenome.Athaliana.TAIR.TAIR10.1.html and tried to install
But I gets an error message when I tried to install.
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("BSgenome.Athaliana.TAIR.TAIR10.1")
Warning message:
package 'BSgenome.Athaliana.TAIR.TAIR10.1' is not available for Bioconductor version '3.12'
A version of this package for your version of R might be available elsewhere
Feedback is greatly appreciated.
Thank you.
Hello,
Thank you very much for your response. I should have mentioned this in my initial post. I started with R 4.2 and Bioc 3.15. I was unable to install it and got the same error. Then I used 3.12 as it was given in the link https://bioconductor.statistik.tu-dortmund.de/packages/3.12/data/annotation/html/BSgenome.Athaliana.TAIR.TAIR10.1.html
If you could please provide a link for new version it will be helpful.
Thank you.
Oh, right. We did have that package and now it seems to be gone? No idea why that happened. You might try building your own. If you have
BSgenome
installed, there are two useful things in that package.The first file is a 'seed' file that you can use as a template to build a package for yourself. You would likely need to make some modifications, but it's what Herve used in the past so I assume it should still work. The second is a directory that contains some R code to parse the FASTA file into a format useful for building the package.
Those two things, plus the vignette for building a package should be sufficient to get one for yourself.