Originally posted by dmacmillan
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Originally posted by dmacmillan
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If you set '--readNum 50' instead, it will produce the number of windows required to have, on average, 50 reads per window in the sample with least number of reads. In this case, larger sam/bam files will produce larger tab files
WARNING! CNAnorm was designed for low coverage data. In particular, if you have large bam files and set parameters to have MANY windows, function peakPloidy and addDNACopy will take very long.
There are ways to solve this, I might write a tutorial in future...
Originally posted by dmacmillan
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Code:
toSkip <- c("chrY", "chrM")
Code:
toSkip <- c("Y", "M")
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