I’m trying use the Extract Genomic DNA tool and keep getting the error: 2347 warnings, 1st is: Chromosome by name ‘chr14’ was not found for build ‘hg19’.
Skipped 2347 invalid lines, 1st is #1, “chr14 100241205 100241705 region_0 0 +” Also see attached screenshot of output.
The input file is a bed file after using bedtools intersect intervals and the reference genome used was hg19. Is there a formatting issue with the bed file? Does it need to be converted to a different file type or format in order for the Extract Genomic DNA tool to work?