Question

CpG density in MEDIPS

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saripalligautam86 ▴ 10

@saripalligautam86-17723

Last seen 6.0 years ago

Dear All,

I am analyzing CpG coverage/density in wheat samples using the MEDIPS package. However, due to some technical reasons, I could not calculate CpG density using the coupling set function of MeDIPS. Although I am trying to do it by making some changes.

I would like to know that instead of calculating CpG density using Coupling set function if I calculate whole genome coverage for single sample (MSet) using the MEDIPS.meth function, can I used the .bam counts for each window as CpG density in that particular MEDIP.Set/sample?

Regards,

CpG MEDIPS • 1.4k views

ADD COMMENT • link 6.1 years ago saripalligautam86 ▴ 10

score 0 · Answer 1 · 2018-10-18

Hi Gautam, The bam counts for each window do not give you information about the number of CpGs in that window. All the best, Lukas _____________________________________ Lukas Chavez, Ph.D. Assistant Professor, Department of Medicine University of California, San Diego (UCSD) Biomedical Research Facility 2 | Room 2A24 9500 Gilman Drive | MC 0765 | La Jolla, CA 92093 T: 858 246 1919 | Email: lukaschavez@ucsd.edu<mailto:lukaschavez@ucsd.edu> www.oncoepigenomics.org<http: www.oncoepigenomics.org=""> On Oct 18, 2018, at 3:18 AM, saripalligautam86 [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User saripalligautam86<https: support.bioconductor.org="" u="" 17723=""/> wrote Question: CpG density in MEDIPS<https: support.bioconductor.org="" p="" 114145=""/>: Dear All, I am analyzing CpG coverage/density in wheat samples using the MEDIPS package. However, due to some technical reasons, I could not calculate CpG density using the coupling set function of MeDIPS. Although I am trying to do it by making some changes. I would like to know that instead of calculating CpG density using Coupling set function if I calculate whole genome coverage for single sample (MSet) using the MEDIPS.meth function, can I used the .bam counts for each window as CpG density in that particular MEDIP.Set/sample? Regards, ________________________________ Post tags: CpG, MEDIPS You may reply via email or visit CpG density in MEDIPS

score 0 · Answer 2 · 2018-10-18

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saripalligautam86 ▴ 10

@saripalligautam86-17723

Last seen 6.0 years ago

Thanks Lukas. In that case, can you please let me know what those bam counts actually indicate and how is the log fold change actually calculated using MEDIPS.meth? Regards,

ADD COMMENT • link 6.1 years ago saripalligautam86 ▴ 10

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Hi Gautam, Please see pages 14-15 of the Reference Manual for a description of the values returned by the MEDIPS.meth function (including the counts and log fold change values). Please let me know in case you have further questions. All the best, Lukas _____________________________________ Lukas Chavez, Ph.D. Assistant Professor, Department of Medicine University of California, San Diego (UCSD) Biomedical Research Facility 2 | Room 2A24 9500 Gilman Drive | MC 0765 | La Jolla, CA 92093 T: 858 246 1919 | Email: lukaschavez@ucsd.edu<mailto:lukaschavez@ucsd.edu> www.oncoepigenomics.org<http: www.oncoepigenomics.org=""> On Oct 18, 2018, at 10:17 AM, saripalligautam86 [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User saripalligautam86<https: support.bioconductor.org="" u="" 17723=""/> wrote Answer: CpG density in MEDIPS<https: support.bioconductor.org="" p="" 114145="" #114168="">: Thanks Lukas. In that case, can you please let me know what those bam counts actually indicate and how is the log fold change actually calculated using MEDIPS.meth? Regards, ________________________________ Post tags: CpG, MEDIPS You may reply via email or visit A: CpG density in MEDIPS

ADD REPLY • link 6.1 years ago Lukas Chavez ▴ 570

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Thanks Lukas,

After reading the reference manual, I understand that .bam counts are the probable reads that are methylated (reads containing the methylated CpGs) if I am not wrong. You may please correct me if required. However, I am still confused what are the logCPM values that are also returned during the differential coverage/methylation analysis using MEDIPS.meth?

Further, is it possible to include custom annotation file (possible GTF or GFF3 format) for annotation analysis using MEDIPS? Because, wheat annotation is perhaps not available in Biomart.

Regards,

ADD REPLY • link 6.1 years ago saripalligautam86 ▴ 10