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Q&A forum for methylKit related issues. You can directly e-mail your questions to methylkit_discussion@googlegroups.com (no need for google account) or post a question using the web interface and rich formatting (google account needed)

please try to send a reproducible example with your question whenever possible. This will help us understand your question better.

methylkit.googlecode.com

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Sangeeta Kumari, saman jones3

May 2

Thank you for the reply. I have few queries regarding the result. I got the result given below. when

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Thank you for the reply. I have few queries regarding the result. I got the result given below. when

May 2

JWonder B2Blithe, Alexander Blume9

Apr 30

Function unite unable to work

got it, thanks! On Tuesday, April 30, 2024 at 3:21:16 AM UTC-4 Alexander Blume wrote: Also, the

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Function unite unable to work

got it, thanks! On Tuesday, April 30, 2024 at 3:21:16 AM UTC-4 Alexander Blume wrote: Also, the

Apr 30

Apr 29

Recall: Inherited method for function ‘unite’

edit...@vt.edu would like to recall the message, "Inherited method for function 'unite

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Recall: Inherited method for function ‘unite’

edit...@vt.edu would like to recall the message, "Inherited method for function 'unite

Apr 29

Apr 29

Inherited method for function ‘unite’

Hello, I am trying to use methylkit for differential analysis on data I have processed already with

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Inherited method for function ‘unite’

Hello, I am trying to use methylkit for differential analysis on data I have processed already with

Apr 29

Alejandro, … Juan Pablo Aguilar Cabezas13

Apr 25

associating DM-CpG, gene part, delta_methylation with a GENE NAME

Alejandro, Were you able to do your analysis? I am interested in doing the same, I want to find the

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associating DM-CpG, gene part, delta_methylation with a GENE NAME

Alejandro, Were you able to do your analysis? I am interested in doing the same, I want to find the

Apr 25

Apr 23

How to concat methbase objects?

Nevermind, I have already asked this question! On Tuesday 23 April 2024 at 17:25:09 UTC+2 Ryan

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How to concat methbase objects?

Nevermind, I have already asked this question! On Tuesday 23 April 2024 at 17:25:09 UTC+2 Ryan

Apr 23

Neel Aluru, … Alexander Blume14

Apr 10

diffMethPerChr - exclude and ideoDMC

Hi Tuba, The myDiff25p object contains this information. If you want the ranges, you could convert it

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diffMethPerChr - exclude and ideoDMC

Hi Tuba, The myDiff25p object contains this information. If you want the ranges, you could convert it

Apr 10

Apr 8

Question about overdispersion and covariates

Hi, I am currently calculating the differential methylation of samples (8 control, 9 treated), using

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Question about overdispersion and covariates

Hi, I am currently calculating the differential methylation of samples (8 control, 9 treated), using

Apr 8

leulmi selma, Altuna Akalin2

Mar 26

Annotation error

I think this needs to be a bed12 file, regular hgTable structure might not work, please send a

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Annotation error

I think this needs to be a bed12 file, regular hgTable structure might not work, please send a

Mar 26

kyuri, Alexander Blume2

Mar 13

I would like to create the BED12 file needed for annotation from a gtf or gff3 file.

Hi kyuri, Please see the previous post regarding this issue: https://groups.google.com/g/

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I would like to create the BED12 file needed for annotation from a gtf or gff3 file.

Hi kyuri, Please see the previous post regarding this issue: https://groups.google.com/g/

Mar 13

Uxue Lazkano, Alexander Blume2

Mar 13

Merging tiles before differential methylation analysis in methylKit

Hi Uxue, Currently, there is no methylKit function to merge overlapping intervals. However, you can

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Merging tiles before differential methylation analysis in methylKit

Hi Uxue, Currently, there is no methylKit function to merge overlapping intervals. However, you can

Mar 13

Ans Afzal, Alexander Blume2

Feb 14

downstream analysis by edgeR for DNA methylation; WGBS

Hi Ans, This is not the correct forum to ask for edgeR-related questions. Please check out the edgeR

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downstream analysis by edgeR for DNA methylation; WGBS

Hi Ans, This is not the correct forum to ask for edgeR-related questions. Please check out the edgeR

Feb 14

leulmi selma, … Altuna Akalin7

Feb 14

methylKit with nanopore WGS

Please let us know how it goes. We don't have experience with nanopore yet but if you can get a

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methylKit with nanopore WGS

Please let us know how it goes. We don't have experience with nanopore yet but if you can get a

Feb 14

David Fisher, Alexander Blume3

Jan 14

Correct model specification for paired design

OK thank you, and apologies for not searching properly before asking. David On Thursday, January 11,

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Correct model specification for paired design

OK thank you, and apologies for not searching properly before asking. David On Thursday, January 11,

Jan 14

Julian Marchesi, Alexander Blume2

Jan 11

Re PCAsamples(meth)

Hi Julian, The PCA is calculated from the matrix of per-base methylation percentage over the samples

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Re PCAsamples(meth)

Hi Julian, The PCA is calculated from the matrix of per-base methylation percentage over the samples

Jan 11

Loryn Smith, … Manoswini Dash4

Jan 9

error when trying to do a PCA (from uniting them)

Hi I am recently having the similar issue. I have data with more NA values (when I run with min.per.

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error when trying to do a PCA (from uniting them)

Hi I am recently having the similar issue. I have data with more NA values (when I run with min.per.

Jan 9

Muhyiddeen Muazu

12/7/23

Annotating enhancers, 5' and 3'UTRs

Hi all! I am analyzing RRBS data, and I wanted to use methylkit & genomation to annotate

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Annotating enhancers, 5' and 3'UTRs

Hi all! I am analyzing RRBS data, and I wanted to use methylkit & genomation to annotate

12/7/23

Muhyiddeen Muazu, Alexander Blume3

12/7/23

How do i Retrieve Percentage methylation for just differentially methylayed CpGs

Thank you very much Alex. It worked very well, although I did not use the pipe but rather I did it in

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How do i Retrieve Percentage methylation for just differentially methylayed CpGs

Thank you very much Alex. It worked very well, although I did not use the pipe but rather I did it in

12/7/23

10/30/23

methylkit question

My name is Nilanjana. I am analyzing Enzymatic Methylation sequencing data using methylKit package.

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methylkit question

My name is Nilanjana. I am analyzing Enzymatic Methylation sequencing data using methylKit package.

10/30/23

10/18/23

are promoter region counts counted twice? and some additional minor questions

Dear Methylkit Team and Community, I am currently analysing mouse sperm methylation data, comparing a

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are promoter region counts counted twice? and some additional minor questions

Dear Methylkit Team and Community, I am currently analysing mouse sperm methylation data, comparing a

10/18/23

Lei Jiang, … Alexander Blume4

10/9/23

assembly and annotation bed file

Hi, for any gff-based annotation prepared with gffToGRanges() please use `annotateWithFeatures()`

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assembly and annotation bed file

Hi, for any gff-based annotation prepared with gffToGRanges() please use `annotateWithFeatures()`

10/9/23

David Fisher, Alexander Blume4

10/9/23

Empty tabix files from regionCounts

Hi David, The segfault error indicates we are running out of memory. The traceback shows that the

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Empty tabix files from regionCounts

Hi David, The segfault error indicates we are running out of memory. The traceback shows that the

10/9/23

9/27/23

Problems with calculateDiffMeth

Good afternon everyone, I'm having probles using calculateDiffMeth() function. I get the

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Problems with calculateDiffMeth

Good afternon everyone, I'm having probles using calculateDiffMeth() function. I get the

9/27/23

Lei Jiang, … Georges Kanaan5

9/26/23

Differentially methylated genes

Hi Lei, I was wondering if you could share the code that ended up working for you when using

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Differentially methylated genes

Hi Lei, I was wondering if you could share the code that ended up working for you when using

9/26/23

9/18/23

comparison between groups with subgroup and replicate

Dear methylKit author and everyone, May I ask you something regarding analysis method using methylKit

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comparison between groups with subgroup and replicate

Dear methylKit author and everyone, May I ask you something regarding analysis method using methylKit

9/18/23

Uxue Lazkano, Alexander Blume6

9/11/23

Problems with methRead function when reading a .txt report

Thanks Alex, all solved! I am very grateful for the help you have given me. All the best, Uxue El

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Problems with methRead function when reading a .txt report

Thanks Alex, all solved! I am very grateful for the help you have given me. All the best, Uxue El

9/11/23

Mark Ezegbogu, … Mark Ezegbogu9

9/8/23

Annotation query

All working now! You're the real deal, Alex!!!! Muchos gracias!!! Mark. On Saturday, September 9,

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Annotation query

All working now! You're the real deal, Alex!!!! Muchos gracias!!! Mark. On Saturday, September 9,

9/8/23

Yumary V., Alexander Blume2

9/8/23

Using methylkit filter out signal from another sample

Hi Yumary, Not sure if this works, but you might achieve this using the `adjustMethylC` function (

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Using methylkit filter out signal from another sample

Hi Yumary, Not sure if this works, but you might achieve this using the `adjustMethylC` function (

9/8/23

NH, … Alexander Blume6

9/8/23

What Columns and files are accepted for MethylKit

Hi UL, This seems to be a different issue. Please send the code you used and the output, otherwise,

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What Columns and files are accepted for MethylKit

Hi UL, This seems to be a different issue. Please send the code you used and the output, otherwise,

9/8/23

TJ Sou, Alexander Blume2

9/8/23

start=end or fixed wiedth

Hi TJ, The default analysis mode in methylKit will be CpG-base-centric, thus having the same start

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start=end or fixed wiedth

Hi TJ, The default analysis mode in methylKit will be CpG-base-centric, thus having the same start

9/8/23

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