Question

karyoploteR genome coverage plotting using BSgenome.TAIR10

0

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rtt100 • 0

@911b91ef

Last seen 2.2 years ago

United States

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.

BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome • 1.8k views

ADD COMMENT • link updated 2.2 years ago by James W. MacDonald 67k • written 2.2 years ago by rtt100 • 0

1

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bernatgel ▴ 150

@bernatgel-7226

Last seen 24 days ago

Spain

Hi

If you only want to use it to plot with karyoploteR, you do not actually need a full BSgenome. You can simply create a GRanges object or a bed-like file with the chromosome names and lengths and give it as the genome to plotKaryotype as if it were a custom genome. It's not ideal, but will work.

There's more information on https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CustomGenomes/CustomGenomes.html

Hope this helps

ADD COMMENT • link 2.2 years ago bernatgel ▴ 150

score 3 · Accepted Answer · 2022-09-27

3

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 19 hours ago

United States

We are on Bioc 3.15, which has TAIR10, so you need to update your R and Bioconductor installation.

ADD COMMENT • link 2.2 years ago James W. MacDonald 67k

0

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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.

ADD REPLY • link 2.2 years ago rtt100 • 0

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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.

> library(BSgenome)
> thedir <- system.file("extdata/GentlemanLab/", package = "BSgenome")
> dir(thedir, "TAIR10")
[1] "BSgenome.Athaliana.TAIR.TAIR10.1-seed" 
[2] "BSgenome.Athaliana.TAIR.TAIR10.1-tools"

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.

ADD REPLY • link 2.2 years ago James W. MacDonald 67k

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> download.file("https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.4_TAIR10.1/GCF_000001735.4_TAIR10.1_genomic.fna.gz", "GCF_000001735.4_TAIR10.1_genomic.fna.gz")
trying URL 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.4_TAIR10.1/GCF_000001735.4_TAIR10.1_genomic.fna.gz'
Content type 'application/x-gzip' length 37482339 bytes (35.7 MB)
downloaded 35.7 MB

## this next bit is the code in the tools dir
> library(Biostrings)
> library(GenomeInfoDb)

> TAIR10.1 <- readDNAStringSet("GCF_000001735.4_TAIR10.1_genomic.fna.gz")
> current_RefSeqAccn <- unlist(heads(strsplit(names(TAIR10.1), " ", fixed=TRUE), n=1L))
> chrominfo <- getChromInfoFromNCBI("TAIR10.1")
> expected_RefSeqAccn <- chrominfo[ , "RefSeqAccn"]
> stopifnot(identical(expected_RefSeqAccn, current_RefSeqAccn))
> names(TAIR10.1) <- chrominfo[ , "SequenceName"]
> 
> for (i in seq_along(TAIR10.1)) {
+     filename <- paste0(names(TAIR10.1)[[i]], ".fa")
+     cat("writing ", filename, "\n", sep="")
+     writeXStringSet(TAIR10.1[i], file=filename, width=50L)
+ }
writing 1.fa
writing 2.fa
writing 3.fa
writing 4.fa
writing 5.fa
writing MT.fa
writing Pltd.fa

## then I copied the seed file from the BSgenome dir to my working dir
## and changed the line that starts with seqs_srcdir: to be the same as the working dir
> library(BSgenome)
> forgeBSgenomeDataPkg("BSgenome.Athaliana.TAIR.TAIR10.1-seed")
Creating package in ./BSgenome.Athaliana.TAIR.TAIR10.1 
Saving 'seqlengths' object to compressed data file './BSgenome.Athaliana.TAIR.TAIR10.1/inst/extdata/seqlengths.rds' ... DONE
Loading FASTA file 'C:/Users/jmacdon/Desktop//1.fa' ... DONE
Saving '1' object to compressed data file './BSgenome.Athaliana.TAIR.TAIR10.1/inst/extdata/1.rds' ... DONE
Loading FASTA file 'C:/Users/jmacdon/Desktop//2.fa' ... DONE
Saving '2' object to compressed data file './BSgenome.Athaliana.TAIR.TAIR10.1/inst/extdata/2.rds' ... DONE
Loading FASTA file 'C:/Users/jmacdon/Desktop//3.fa' ... DONE
Saving '3' object to compressed data file './BSgenome.Athaliana.TAIR.TAIR10.1/inst/extdata/3.rds' ... DONE
Loading FASTA file 'C:/Users/jmacdon/Desktop//4.fa' ... DONE
Saving '4' object to compressed data file './BSgenome.Athaliana.TAIR.TAIR10.1/inst/extdata/4.rds' ... DONE
Loading FASTA file 'C:/Users/jmacdon/Desktop//5.fa' ... DONE
Saving '5' object to compressed data file './BSgenome.Athaliana.TAIR.TAIR10.1/inst/extdata/5.rds' ... DONE
Loading FASTA file 'C:/Users/jmacdon/Desktop//MT.fa' ... DONE
Saving 'MT' object to compressed data file './BSgenome.Athaliana.TAIR.TAIR10.1/inst/extdata/MT.rds' ... DONE
Loading FASTA file 'C:/Users/jmacdon/Desktop//Pltd.fa' ... DONE
Saving 'Pltd' object to compressed data file './BSgenome.Athaliana.TAIR.TAIR10.1/inst/extdata/Pltd.rds' ... DONE

> install.packages("BSgenome.Athaliana.TAIR.TAIR10.1", repos = NULL, type = "source")
Installing package into 'C:/Users/jmacdon/AppData/Local/R/win-library/4.2'
(as 'lib' is unspecified)
* installing *source* package 'BSgenome.Athaliana.TAIR.TAIR10.1' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
package 'GenomeInfoDb' was built under R version 4.2.1 
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: package 'GenomeInfoDb' was built under R version 4.2.1
** testing if installed package can be loaded from final location
Warning: package 'GenomeInfoDb' was built under R version 4.2.1
** testing if installed package keeps a record of temporary installation path
* DONE (BSgenome.Athaliana.TAIR.TAIR10.1)

## et voila!

ADD REPLY • link 2.2 years ago James W. MacDonald 67k