BSgenome forging -- not valid BSgenomeDataPkgSeed slots
1
0
Entering edit mode
qiwang1993 • 0
@qiwang1993-7195
Last seen 9.3 years ago
China

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.

 

 

 

bsgenome • 2.5k views
ADD COMMENT
0
Entering edit mode

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. 

ADD REPLY
0
Entering edit mode
qiwang1993 • 0
@qiwang1993-7195
Last seen 9.3 years ago
China

hi,

I use single fasta files and get a right result ,But i didnot know the reason why cause the trouble.

Thanks!

 

 

ADD COMMENT

Login before adding your answer.

Traffic: 634 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6