x chromosome CNV analysis

broadinstitute / gistic2

Genomic Identification of Significant Targets in Cancer (GISTIC), version 2

MIT License

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x chromosome CNV analysis #16

Open MAKADDOURA opened 2 years ago

MAKADDOURA commented 2 years ago

Hi. I am trying to format my seg file to run CNV analysis on chromosome X. I've tried leaving the "chromosome" column notation as "X" and converted "X" to 23, however both attempts were unsuccessful with different kinds of errors encountered. When i assign 23 to chromosome X, the run is works, however it includes output on all chromosomes except X. The reference genome I am using is hg19. Any thoughts as what may be wrong? Thanks!

lichennan123 commented 3 months ago

I had the same question.... Did you ever find the answer?