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akdess / CaSpER

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Annotation file for hg38 #63

Closed Troyee13 closed 3 years ago

Troyee13 commented 3 years ago

Hello, I have my own set of bulk RNA seq BAM files analysed with hg38 genome. Please elaborate on how to generate an annotation file for hg38 with Caspe. Thanks

Troyee13 commented 3 years ago

I have figured it out. No issue.

lifan18 commented 2 years ago

I have figured it out. No issue.

Hi Troyee, I have the same issue to generate a right annotation file for hg38. I used the following code to make this file, however, it cannot be used properly in the later process.

annotation <- generateAnnotation(id_type="hgnc_symbol", genes=rownames(scRNA@assays$RNA@data), centromere=centromere, ishg19 = T)

Then, errors came in CreateCasperObject There were 50 or more warnings (use warnings() to see the first 50) and in final.objects final.objects <- runCaSpER(object, removeCentromere=T, cytoband=cytoband, method="iterative") Performing recursive median filtering... Performing HMM segmentation... Error in DataFrame(..., check.names = FALSE) : different row counts implied by arguments

Did you get any solution?

Thank you!