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haibol2016 / ArchR_utilities

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Issues in create_geneAnnotation_genomeAnnotation.R #1

Closed hukai916 closed 2 years ago

hukai916 commented 2 years ago
  1. In the makeTxDbFromGFF(), the "chrominfo" must not start with "chr", otherwise won't pass makeTxDbFromGFF::.tidy_seqinfo() for some reason. I have to use: chrominfo<-data.frame(chrom=gsub('^chr','',names(chrom_len)), length=unname(chrom_len), is_circular=is_circular)
  2. In the forgeTxDb(), I assume "organism = genome_metadata$genome_metadata," should be "organism = genome_metadata$organism,"
  3. In the forgeTxDb(), "close(gtf)" should be "close(in_gtf)"; also, makeTxDbFromGFF() can take raw file as input, so creating "in_gtf" seems redundant.
  4. In the forgeTxDb(), "paste0(BSgenome, "TxDb.sqlite"))" is problematic, should use a character string to replace BSgenome.