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Hi everyone,
I tried to create a BSgenome data package for maize, and met some troubles.
I created a directory include two files :
maize.2bit (generation by faToTwoBit)
maize.seed (seed file)
Package: BSgenome.zmv2
Title: Full genome sequences for zea mays ( version 2.0)
Description: Full genome sequences for zea mays (maize) as provided by MaizeGDB and stored in Biostrings objects.
Version: 1.0.00
organism: Zea mays ssp.
species: plant
provider: MaizeGDB
provider_version: zmv2
release_date: Dec. 2014
release_name: Maize Genome Sequencing B73 2.0
source_url: ./
organism_biocview: maize
BSgenomeObjname: maize
PkgExamples: genome$GL1000000
BSgenomeObjname: zmv2
seqs_srcdir: /home/user/zmv2
seqfile_name: maize.2bit
when type "forgeBSgenomeDataPkg("maize.seed")" in R , I get a error message :
Error in makeS4FromList("BSgenomeDataPkgSeed", x) :
some names in 'x' are not valid BSgenomeDataPkgSeed slots (SrcDataFiles)
I'd appreciate help to understand what's wrong. Thanks in advance.
Hi,
I cannot reproduce this. What version of BSgenome are you using? Make sure you use the latest (version 1.34.0, part of Bioconductor 3.0). Note that the
BSgenomeObjname
field appears twice in your seed file, which is likely to cause trouble.H.