MFG

[YibingZeng]

Could you give me more specific explanation about the meaning of the standard output? Could you please give me the full name of the following items?

  sense_ave_mC    
  sense_sum_mC    
  sense_sum_NO    
  anti_ave_mC     
  anti_sum_mC  
  anti_sum_NO     
  total_ave_mC  
  total_sum_mC    
  total_sum_NO   

[guoweilong]

sense_ave_mC : the average methylation levels on sense stand sense_sum_mC : sum of methylation levels on sense stand sense_sum_NO : count of the C sites on sense stand Thus, sense_ave_mC = sense_sum_mC / sense_sum_NO. Then you can check with sense_sum_NO when sense_ave_mC is too high.

Then, "anti" indicates the "antisense strand", "total" indicates the "both strands together + sense strand + antisense strand".

Best, Weilong

At 2020-01-15 10:42:04, "Yibing" notifications@github.com wrote:

Could you give me more specific explanation about the meaning of the standard output? Could you please give me the full name of the following items?

sense_ave_mC sense_sum_mC sense_sum_NO anti_ave_mC anti_sum_mC anti_sum_NO total_ave_mC total_sum_mC total_sum_NO

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[YibingZeng]

When I used cgmaptools to calculated the methylation level in a given region, the region file only contained "+" strand, but the result returned the methylation from both strand. The command I used is as followed:

gunzip -c ${I} | cgmaptools mfg -r ${R1} -c 1 -x CG > F_Oh7Brep1_3k_CG_F.mfg

[guoweilong]

Hi Yibing,

cgmaptools will suppose your input regions are strand-specific. Thus for your case, the lines start with "sense" corresponds to your "+" strand; and lines start with "total" corresponds with "two strand together" (equal to "not strand-specific").

Best, Weilong