Question

How to construct a BSgenome object from a custom genome assembly using BSgenomeForge?

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mat149 ▴ 80

@mat149-11450

Last seen 6 weeks ago

United States

Hi,

I have a custom genome assembly contained in .fasta format. Sequences for each of the chromosomes are compiled into a single .fasta file. I'd like to forge a BSgenome object for this genome assembly (not publicly available) I've looked through the vignette and I'm stuck on how to construct the seed object. I know how to generate a BSgenome object using forgeBSgenomeDataPkgFromNCBI(), but I'm stuck on how to construct a BSgenome object from a genome assembly without an accession. Can anyone guide me through the next steps?

Thanks!

setwd("C:\\...\\Desktop\\wd\\dump\\seqs_srcdir")

e122<-readDNAStringSet("E122.fasta", format="fasta",use.names=TRUE)

chroms<-Seqinfo(
    seqnames=c("chrA","chrB","chrC","chrD","chrE","chrF","chrMT"),
    seqlengths=width(e122),
    isCircular=as.logical(c("FALSE","FALSE","FALSE","FALSE","FALSE","FALSE","TRUE"),
    genome=c("E122","E122","E122","E122","E122","E122","E122")))

chroms
Seqinfo object with 7 sequences (1 circular) from an unspecified genome:
  seqnames seqlengths isCircular genome
  chrA        2326463      FALSE   <NA>
  chrB        3127439      FALSE   <NA>
  chrC        3366774      FALSE   <NA>
  chrD        3699297      FALSE   <NA>
  chrE        4325132      FALSE   <NA>
  chrF        4126616      FALSE   <NA>
  chrMT         47890       TRUE   <NA>

BSgenome BSgenomeForge • 344 views

ADD COMMENT • link updated 7 weeks ago by James W. MacDonald 68k • written 7 weeks ago by mat149 ▴ 80

score 0 · Answer 1 · 2025-09-12

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James W. MacDonald 68k

@james-w-macdonald-5106

Last seen 17 hours ago

United States

There is an example in the help page for forgeBSgenomePkgFromTwobitFile. Have you tried emulating that?

ADD COMMENT • link 7 weeks ago James W. MacDonald 68k

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I've tried the following, but I must be missing something:

setwd("C:\\Users\\....\\wd\\dump\\seqs_srcdir")

e122<-readDNAStringSet("E122.fasta", format="fasta",use.names=TRUE)
    # export(e122, "e122.2bit", format = "2bit")

chroms<-Seqinfo(
    seqnames=c("A","B","C","D","E","F","MT"),
    seqlengths=width(e122),
    isCircular=as.logical(c("FALSE","FALSE","FALSE","FALSE","FALSE","FALSE","TRUE"),
    genome=c("E122","E122","E122","E122","E122","E122","E122")))

my_file <- read.dcf("seed.txt", fields = NULL, all = FALSE, keep.white = NULL)
write.dcf(my_file , file = "seed.dcf", append = FALSE, useBytes = FALSE, indent = 0.1 * getOption("width"), width = 0.9 * getOption("width"), keep.white = NULL)
forgeBSgenomeDataPkg("seed.dcf")

**Error in .make_Seqinfo_from_genome(genome) : 
  "e122.2bit" 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 my seed.dcf file:

Package: BSgenome.YLE122.2bit
Title: Custom genome for YL
Description: Full genome sequences for YL.
Version: 1.0.0
Author: MT <mt3@gmail.com>
Maintainer: MT <mt3@gmail.com>
organism: YL
common_name: YL
provider: Custom
provider_version: 1
source_url: C:/Users/.../wd/dump/seqs_srcdir
seqs_srcdir: C:/Users/.../wd/dump/seqs_srcdir/e122.2bit
organism_biocview: Y_L
release_date: 2025-09-15
seqnames: c("A","B","C","D","E","F","MT")
genome: e122.2bit
ondisk_seq_format: 2bit

ADD REPLY • link 7 weeks ago mat149 ▴ 80

1

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You are. The reason I pointed you to forgeBSgenomeDataPkgFromTwobitFile is because it's much simpler, doesn't require a seed file, and is the preferred way of making a BSgenome package. In addition, you don't appear to be setting your seed file up correctly anyway. But since the function I have pointed you to only requires the 2bit file, and is easier to use, I am not going to try to figure out where you went wrong, and instead will point you to the new function instead.

ADD REPLY • link 7 weeks ago James W. MacDonald 68k