BSMAP and methylKit
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Claire Morgan
Jul 29, 2013, 9:44:10 AM7/29/13
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Hi,
I would like to use methylKit on the output from BSMAP to determine differentially methylated regions.
I found a blog spot that helps with the integration of an older version of BSMAP with the data (http://zvfak.blogspot.co.uk/2012/10/how-to-read-bsmap-methylation-ratio.html), but with the latest BSMAP release (v2.74), the output from methylratio.py has changed to include 11 headers instead of 9.
Can you let me know how the old headers 'total_C' and 'methy_C' link to the newer headers 'eff_CT_count', 'C_count' and 'CT_count'. Based on the readme file i think 'total_C' is the same as 'eff_CT_count' and 'methy_C' is the same as 'C_count', but i can't be sure.
Thank you in advance for your help,
Claire
I would like to use methylKit on the output from BSMAP to determine differentially methylated regions.
I found a blog spot that helps with the integration of an older version of BSMAP with the data (http://zvfak.blogspot.co.uk/2012/10/how-to-read-bsmap-methylation-ratio.html), but with the latest BSMAP release (v2.74), the output from methylratio.py has changed to include 11 headers instead of 9.
Can you let me know how the old headers 'total_C' and 'methy_C' link to the newer headers 'eff_CT_count', 'C_count' and 'CT_count'. Based on the readme file i think 'total_C' is the same as 'eff_CT_count' and 'methy_C' is the same as 'C_count', but i can't be sure.
Thank you in advance for your help,
Claire
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