Differential methylation for each annotated region (Bed file) header interpretation

[freedomq8]

Hi there,

thanks for your efforts to make my analysis easy along with lengthy explanation page. I am looking at the final differential methylation results using BED file and I have a question regarding headers and what do they mean:

#region sequence start stop SRR2052492 (treatment) SRR2052493 (treatment) SRR2052494 (treatment) SRR2052495 (treatment) SRR2052496 (treatment) SRR2052487 (control) SRR2052488 (control) SRR2052489 (control) SRR2052490 (control) SRR2052491 (control) treatment average control average log2FC(treament/control) p-value q-value MEG3 chr14 101291953 101292257 1455768/2043201 1636631/3258147 1497615/2643988 1278819/2677687 1699837/1958100 960649/2260743 1655354/3623531 1234101/2867390 1729232/3490690 2112253/4771083 0.6015893811705044 0.45208907524094044 0.4121720465419593 0.032485239405786 0.054142065676310004 CDKN1A chr6 36645463 36645696 106164/169351 67574/108667 39848/111440 70332/114278 56000/82614 184466/257701 135047/184961 153820/212228 90107/139840 97084/153940 0.5797185981069327 0.6962631895179566 -0.264279982267956 0.06970890125229327 0.0871361265653666 IRS1 chr2 227659612 227659781 471/1525 493/1510 556/2015 240/861 534/2047 326/818 325/1045 455/1336 680/1600 607/2070 0.2882633827594873 0.34837676517688165 -0.27326082007437236 0.031291095111098274 0.054142065676310004 INS chr11 2182552 2182775 133094/209138 291969/567402 119026/425194 152310/651761 177366/278973 80460/481158 165062/765934 174273/633564 169227/724203 288122/1036615 0.40974354597583645 0.2408760847942344 0.7664300613080263 0.022056895484407948 0.054142065676310004 PDE7B chr6 136172766 136172917 358560/2258785 151970/1578967 368147/2086541 104049/1062921 506169/2399992 119657/960632 197487/1205221 168450/1002387 197266/1376956 112174/1444852 0.15860896202767896 0.1327258145510687 0.2570252958195374 0.6929437289294518 0.6929437289294518

For example (i am using the results output from the manual section) i am not sure if i understand what is written beneath each sample at a certain target region

• SRR2052492 (treatment) column at MEG3 region its says 1455768/2043201 what does that mean ? number of cytosine levels / total depth ?

• also log2FC(treament/control) column the values ranges from -1 to 1 what does it mean to have a negative and a positive value in terms of methylation ? for example if the value is -0.3 what does that mean ? and if its 0.8 what does that mean in terms of methylation?

Thanks

[osvaldogc]

Hello ! I am answering your questions between your lines below. osvaldo

…

________________________________ From: freedomq8 [notifications@github.com] Sent: Monday, August 10, 2020 5:05 PM To: sing-group/bicycle Cc: Subscribed Subject: [sing-group/bicycle] Differential methylation for each annotated regionBed file) header interpretation (#8) CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe Hi there, thanks for your efforts to make my analysis easy along with lengthy explanation page. I am looking at the final differential methylation results using BED file and I have a question regarding headers and what do they mean: #region sequence start stop SRR2052492 (treatment) SRR2052493 (treatment) SRR2052494 (treatment) SRR2052495 (treatment) SRR2052496 (treatment) SRR2052487 (control) SRR2052488 (control) SRR2052489 (control) SRR2052490 (control) SRR2052491 (control) treatment average control average log2FC(treament/control) p-value q-value MEG3 chr14 101291953 101292257 1455768/2043201 1636631/3258147 1497615/2643988 1278819/2677687 1699837/1958100 960649/2260743 1655354/3623531 1234101/2867390 1729232/3490690 2112253/4771083 0.6015893811705044 0.45208907524094044 0.4121720465419593 0.032485239405786 0.054142065676310004 CDKN1A chr6 36645463 36645696 106164/169351 67574/108667 39848/111440 70332/114278 56000/82614 184466/257701 135047/184961 153820/212228 90107/139840 97084/153940 0.5797185981069327 0.6962631895179566 -0.264279982267956 0.06970890125229327 0.0871361265653666 IRS1 chr2 227659612 227659781 471/1525 493/1510 556/2015 240/861 534/2047 326/818 325/1045 455/1336 680/1600 607/2070 0.2882633827594873 0.34837676517688165 -0.27326082007437236 0.031291095111098274 0.054142065676310004 INS chr11 2182552 2182775 133094/209138 291969/567402 119026/425194 152310/651761 177366/278973 80460/481158 165062/765934 174273/633564 169227/724203 288122/1036615 0.40974354597583645 0.2408760847942344 0.7664300613080263 0.022056895484407948 0.054142065676310004 PDE7B chr6 136172766 136172917 358560/2258785 151970/1578967 368147/2086541 104049/1062921 506169/2399992 119657/960632 197487/1205221 168450/1002387 197266/1376956 112174/1444852 0.15860896202767896 0.1327258145510687 0.2570252958195374 0.6929437289294518 0.6929437289294518> #region sequence start stop SRR2052492 (treatment) SRR2052493 (treatment) SRR2052494 (treatment) SRR2052495 (treatment) SRR2052496 (treatment) SRR2052487 (control) SRR2052488 (control) SRR2052489 (control) SRR2052490 (control) SRR2052491 (control) treatment average control average log2FC(treament/control) p-value q-value MEG3 chr14 101291953 101292257 1455768/2043201 1636631/3258147 1497615/2643988 1278819/2677687 1699837/1958100 960649/2260743 1655354/3623531 1234101/2867390 1729232/3490690 2112253/4771083 0.6015893811705044 0.45208907524094044 0.4121720465419593 0.032485239405786 0.054142065676310004 CDKN1A chr6 36645463 36645696 106164/169351 67574/108667 39848/111440 70332/114278 56000/82614 184466/257701 135047/184961 153820/212228 90107/139840 97084/153940 0.5797185981069327 0.6962631895179566 -0.264279982267956 0.06970890125229327 0.0871361265653666 IRS1 chr2 227659612 227659781 471/1525 493/1510 556/2015 240/861 534/2047 326/818 325/1045 455/1336 680/1600 607/2070 0.2882633827594873 0.34837676517688165 -0.27326082007437236 0.031291095111098274 0.054142065676310004 INS chr11 2182552 2182775 133094/209138 291969/567402 119026/425194 152310/651761 177366/278973 80460/481158 165062/765934 174273/633564 169227/724203 288122/1036615 0.40974354597583645 0.2408760847942344 0.7664300613080263 0.022056895484407948 0.054142065676310004 PDE7B chr6 136172766 136172917 358560/2258785 151970/1578967 368147/2086541 104049/1062921 506169/2399992 119657/960632 197487/1205221 168450/1002387 197266/1376956 112174/1444852 0.15860896202767896 0.1327258145510687 0.2570252958195374 0.6929437289294518 0.6929437289294518 For example (i am using the results output from the manual section) i am not sure if i understand what is written beneath each sample at a certain target region * SRR2052492 (treatment) column at MEG3 region its says 1455768/2043201 what does that mean ? number of cytosine levels / total depth ? If you open the corresponding *DMC.tsv file, you are going to find several cytosine methylation lines for chr14 (i.e. MEG3). If you add the numerator and denominator values of the chr14 lines for that sample (column), you are going to get the numbers that you showed here for MEG3 in that sample 1455768/2043201. Those represent the "C / CTdepth" ratio. * also log2FC(treament/control) column the values ranges from -1 to 1 what does it mean to have a negative and a positive value in terms of methylation ? for example if the value is -0.3 what does that mean ? and if its 0.8 what does that mean in terms of methylation? The log2FC simply tells you whether the level of methylation is higher in the treatment (+) samples or in the control (-) samples. The numerical value shows to what extent the expression is higher in treatment or control samples. It does not necessarily ranges from -1 to 1, it can be higher, as it depends on the samples expression. 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