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PhanstielLab / plotgardener

https://phanstiellab.github.io/plotgardener/
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Plotgenes() and plottranscript () error in hg38 #101

Closed seyoun209 closed 1 year ago

seyoun209 commented 1 year ago

Hi Nicole,

I tried to fix it, but I could not figure it out. library(plotgardener) library(TxDb.Hsapiens.UCSC.hg38.knownGene)

 plotGenes(
 assembly = "hg38",
 chrom = "chr21", chromstart = 28000000, chromend = 30300000
 )

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'seqlengths': invalid DB file In addition: Warning message: Closing open result set, pending rows `

It happens both plotGenes() and plotTranscripts(). It works with the hg19 but doesn't work with the hg38. Thank you in advance

seyoun209 commented 1 year ago

I installed every possible thing and it seems working now. My bad