Please help adding Xenopus tropicalis to GenomeInfoDb package

[clarkzor]

Hello, I am trying to utilize the "forgeBSgenomeDataPkg("../Xenopustropicalis_Seedfile.dcf")" to create a new package from a seed file, however I receive the error message:

Error in .make_Seqinfo_from_genome(genome) : "xenTro" is not a registered NCBI assembly or UCSC genome (use registered_NCBI_assemblies() or registered_UCSC_genomes() to list the NCBI or UCSC assemblies/genomes currently registered in the GenomeInfoDb package)

This is what my seed file looks like:

Package: BSgenome.Xtrop.NCBI.UCB_Xtro_10.0 Title: Full genomic sequences for Xenopus Tropicalis VIA NCBI Description: For Multiomic Analysis Version: 1.0.0 organism: Xenopus tropicalis common_name: Frog provider: NCBI genome: UCB_Xtro_10.0 release_date: Nov. 2019 source_url: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000004195.4/ organism_biocview: Xenopus_tropicalis BSgenomeObjname: Xtrop seqs_srcdir: /Users/coron/OneDrive/Desktop/10xGenomics/ seqfile_name: UCB_Xtro_10.0_genome.fasta

could you please add the Xenopus tropicalis genome to the GenomeInfoDb package so that I could use this function.

Also, should I be able to run this using a single genomic fasta file that contains information about all the chromosomes, or do I have to actually split up the chromosomes into their own individual fasta files?

Thank you for your help.

[hpages]

The seed file approach has been superseded by the forgeBSgenomeDataPkgFromNCBI() and forgeBSgenomeDataPkgFromUCSC() functions from the new BSgenomeForge package:

library(BSgenomeForge)
forgeBSgenomeDataPkgFromNCBI("GCF_000004195.4", pkg_maintainer="Your Name <your.email@address.com>")

This will create the BSgenome.Xtropicalis.NCBI.UCBXtro10.0 package in the current directory.

Best, H.

[hpages]

Were you able to create the BSgenome.Xtropicalis.NCBI.UCBXtro10.0 package @clarkzor?