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Cannot find the in genome hg38 Maybe a problem of chromosome labels #8

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Edert opened this issue Jul 17, 2023 · 0 comments

Edert commented Jul 17, 2023

Hi,

I wanted to test DEScan2 on hg38 aligned bam files, however it does not seem to work at the countFinalRegions step:

finalRegions <- DEScan2::countFinalRegions(regionsGRanges=regionsGR, readsFilePath=bam.files, fileType="bam", minCarriers=1,genomeName="hg38", onlyStdChrs=TRUE, saveFlag=FALSE,verbose=FALSE) 

Error in setGRGenomeInfo(GRanges = regionsGRanges, genomeName = genomeName) :
  Cannot find the  in genome hg38 Maybe a problem of chromosome labels

How can I resolve this?

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