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wenbostar / PGA

PGA: a tool for ProteoGenomics Analysis
http://wenbostar.github.io/PGA/
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PrepareAnnotationRefseq2 error #3

Closed jaya-share closed 6 years ago

jaya-share commented 6 years ago

Faced error while executing command on R version 3.4.4 customProDB_1.18.0, PGA_1.8.1 Command executed from tutorial

transcript_ids <- c("NM_001126112", "NM_033360", "NR_073499")
pepfasta <- system.file("extdata", "refseq_pro_seq.fasta",
                        package="customProDB")
CDSfasta <- system.file("extdata", "refseq_coding_seq.fasta",
                        package="customProDB")
annotation_path <- tempdir()
PrepareAnnotationRefseq2(genome='hg19', CDSfasta, pepfasta, annotation_path,
                          dbsnp=NULL, transcript_ids=transcript_ids,
                          splice_matrix=FALSE, COSMIC=FALSE)

Build TranscriptDB object (txdb.sqlite) ... Error in .tablename2track(tablename, session) : UCSC table "refGene" is not supported

wenbostar commented 6 years ago

Please use the latest version of PGA in this repository: PGA. We just fixed a few bugs which were caused by the changes of UCSC annotation. Please install the new version using the following code:

install.packages("BiocManager")
BiocManager::install(version = '3.8')
install.package("RMariaDB")
library("BiocManager")
install("Shawn-Xu/PGA")
jaya-share commented 6 years ago

Thanks for the update..it seem to work now!

wenbostar commented 6 years ago

Great.