Originally posted by fkrueger
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It is very kind of you to provide this script to generates a cytosine methylation report. But it does not seems to work, something error like this:
perl genome_wide_cytosine_report.pl --help
Type of arg 1 to keys must be hash (not hash element) at genome_wide_cytosine_report.pl line 119, near "},"
Type of arg 1 to keys must be hash (not hash element) at genome_wide_cytosine_report.pl line 206, near "},"
BEGIN not safe after errors--compilation aborted at genome_wide_cytosine_report.pl line 289.
In my opinion, It is completely necessary to add an option to generate a bedGraph files and cytosine methylation report straight away in methylation extractor .
traditional dinucleotide context may not suitable for our samples, I need trinucleotide classification. As you said, I will call differential methylation on a per-cytosine basis instead of a region. It is will be more meaningful.
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