MethPipe and MethBase Users

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MethPipe is a computational pipeline for analyzing bisulfite sequencing data: http://smithlabresearch.org/software/methpipe
MethBase is a reference methylome database: http://smithlabresearch.org/software/methbase

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3/23/21

Issues installing MethPipe

Hi, I am trying to install MethPipe 4.1.1 on a linux server running Red Hat Enterprise 7.9. I am

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Issues installing MethPipe

Hi, I am trying to install MethPipe 4.1.1 on a linux server running Red Hat Enterprise 7.9. I am

3/23/21

Flavia Marzetta

1/14/21

Radmeth regression computation time

Hi, I am running radmeth regression for the first time on a dataset including 24 samples and about

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Radmeth regression computation time

Hi, I am running radmeth regression for the first time on a dataset including 24 samples and about

1/14/21

12/2/20

Fwd: methstate trouble shutting

Looks like this issue has been resolved. Best regards, Meng ---------- Forwarded message ---------

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Fwd: methstate trouble shutting

Looks like this issue has been resolved. Best regards, Meng ---------- Forwarded message ---------

12/2/20

Quetzely Ortiz, … Xiaojing Ji6

7/23/20

How Radmeth merge define the beggining and the end of a DMR

Hi Quetzely, Thanks for your question! RADMeth considers the correlation between individual sites to

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How Radmeth merge define the beggining and the end of a DMR

Hi Quetzely, Thanks for your question! RADMeth considers the correlation between individual sites to

7/23/20

WAN MILES, Ben Decato6

7/5/20

Methdiff results

Dear Ben, Thank you very much for the suggestions. I was thinking about ranking these DMRs based on

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Methdiff results

Dear Ben, Thank you very much for the suggestions. I was thinking about ranking these DMRs based on

7/5/20

6/19/20

Fwd: methdiff results interpretation

---------- Forwarded message --------- 寄件者： <miles...@gmail.com> Date: 2020年6月18日週四 18:11

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Fwd: methdiff results interpretation

---------- Forwarded message --------- 寄件者： <miles...@gmail.com> Date: 2020年6月18日週四 18:11

6/19/20

4/1/20

HMM training for PMD command

Hi again, I ran pmd for two human samples with distinct global methylation level: sample A: higher

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HMM training for PMD command

Hi again, I ran pmd for two human samples with distinct global methylation level: sample A: higher

4/1/20

Juheon Maeng, Ben Decato3

4/1/20

pmd output (5th column)

Thank you for the clarification! Best regards, Ju Heon Maeng On Wed, Apr 1, 2020 at 3:34 PM Ben

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pmd output (5th column)

Thank you for the clarification! Best regards, Ju Heon Maeng On Wed, Apr 1, 2020 at 3:34 PM Ben

4/1/20

shulil...@cau.edu.cn, … Di Wang10

3/12/20

problem about methcounts

Hi Xiaojing, Thanks for your response. Is it must run with LC_ALL=C? As I understand LC_ALL=C is to

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problem about methcounts

Hi Xiaojing, Thanks for your response. Is it must run with LC_ALL=C? As I understand LC_ALL=C is to

3/12/20

Patrick McGowan, Ben Decato2

1/23/20

qqplots with RADmeth data

Hi Patrick, The negative p-values are just placeholders to say "the hypothesis wasn't tested

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qqplots with RADmeth data

Hi Patrick, The negative p-values are just placeholders to say "the hypothesis wasn't tested

1/23/20

lawrence ong, Andrew D. Smith2

8/22/19

I advise doing both. But yes, you should definitely try radmeth for this situation. Let me know how

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I advise doing both. But yes, you should definitely try radmeth for this situation. Let me know how

8/22/19

2/12/19

MLML, reliable depth

Hi, First I would like to thank you for the very useful tools you provide! I have used the updated

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MLML, reliable depth

Hi, First I would like to thank you for the very useful tools you provide! I have used the updated

2/12/19

Bonnie Cantrell, Ben Decato2

2/8/19

RadMeth Output Meaning

Hi Bonnie, In our modeling, the methylation level ranges from 0 to 1. A methylation difference of -

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RadMeth Output Meaning

Hi Bonnie, In our modeling, the methylation level ranges from 0 to 1. A methylation difference of -

2/8/19

Samantha Schaffner, Meng Zhou6

12/3/18

MLML produces all NaN

Hi Meng, The line "chr X0 X X.1 X0.1 X562912164834048" showed up as a header in my merge-

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MLML produces all NaN

Hi Meng, The line "chr X0 X X.1 X0.1 X562912164834048" showed up as a header in my merge-

12/3/18

keya...@gmail.com, … Xiaojing Ji6

11/28/18

Problem about Methcounts

Hi Ke, Have you been using the test reads data packaged in MethPipe? We had a check and found it to

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Problem about Methcounts

Hi Ke, Have you been using the test reads data packaged in MethPipe? We had a check and found it to

11/28/18

Guosong Wang, Xiaojing Ji (Liz Ji)4

9/22/18

Problems with deduplicate

Hi Guosong, Looks like all binaries from the folder "utils" are missing. Please check if

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Problems with deduplicate

Hi Guosong, Looks like all binaries from the folder "utils" are missing. Please check if

9/22/18

lawrence ong, Ben Decato3

9/13/18

Hi Ben, Thanks for getting back to me. I managed to get it to work. I think it was the presence of

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Hi Ben, Thanks for getting back to me. I managed to get it to work. I think it was the presence of

9/13/18

Patrick McGowan

9/12/18

Effect size and power calculations

Hi There, Is the log-odds ratio output equivalent to the effect size? If so, how can I use this to

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Effect size and power calculations

Hi There, Is the log-odds ratio output equivalent to the effect size? If so, how can I use this to

9/12/18

8/31/18

levels program, frac_meth

Hi, I have a question about computation of fractional methylation level by "levels" program

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levels program, frac_meth

Hi, I have a question about computation of fractional methylation level by "levels" program

8/31/18

Chris S, Meng Zhou5

7/22/18

Thanks again Meng! I appreciate how responsive and helpful everyone has been! I have been using -t

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Thanks again Meng! I appreciate how responsive and helpful everyone has been! I have been using -t

7/22/18

Chris S, … Jianghan Qu3

6/27/18

Radmeth regression for MLML data

Hi Chris, Could you checkout the latest version of methpipe on github? MLML is now part of Methpipe.

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hydroxymethylation

Radmeth regression for MLML data

Hi Chris, Could you checkout the latest version of methpipe on github? MLML is now part of Methpipe.

6/27/18

Patrick McGowan, Andrew D. Smith2

6/26/18

sex chromosome removal steps

I think it should be fine, but you might check how it differs if you use the raw p-values instead of

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sex chromosome removal steps

I think it should be fine, but you might check how it differs if you use the raw p-values instead of

6/26/18

Andrew D. Smith, Ben Decato3

6/26/18

Fwd: RADMeth negative p-values

On Jun 26, 2018, at 12:21 PM, Ben Decato <dec...@usc.edu> wrote: > > Hi Patrick, >

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Fwd: RADMeth negative p-values

On Jun 26, 2018, at 12:21 PM, Ben Decato <dec...@usc.edu> wrote: > > Hi Patrick, >

6/26/18

Chris S, Ben Decato3

6/26/18

Using RRBS and oxo-RRBS data with Merge Methcounts and Radmeth Adjust

Thanks Ben! On Monday, June 25, 2018 at 1:34:34 PM UTC-5, Ben Decato wrote: Hi Chris, Thanks for

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Using RRBS and oxo-RRBS data with Merge Methcounts and Radmeth Adjust

Thanks Ben! On Monday, June 25, 2018 at 1:34:34 PM UTC-5, Ben Decato wrote: Hi Chris, Thanks for

6/26/18

Elitsa Stoyanova, … Chris S3

6/25/18

hydroxymethylation

Hi Jianghan, I think this is related to the original question. The MLML output appears to not be

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hydroxymethylation

Hi Jianghan, I think this is related to the original question. The MLML output appears to not be

6/25/18

Kangli Wang, Meng Zhou2

1/8/18

How to compare amr in different groups

Hi all, This topic has been discussed in our github repo, and I should have let this post come

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How to compare amr in different groups

Hi all, This topic has been discussed in our github repo, and I should have let this post come

1/8/18

hashima...@gmail.com, Jianghan Qu5

10/5/17

Thank you very much for quick replies and clarifications. Regards, Adnan. On Tuesday, October 3, 2017

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Thank you very much for quick replies and clarifications. Regards, Adnan. On Tuesday, October 3, 2017

10/5/17

Tommaso Andreani

9/22/17

Background in Enrichment of DMRs

Hello, I have my set of Hyper and Hypo DMRs from my experiment. I would like to enrich with great

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Background in Enrichment of DMRs

Hello, I have my set of Hyper and Hypo DMRs from my experiment. I would like to enrich with great

9/22/17

Kyle Hernandez, Meng Zhou2

8/31/17

unclear about walt bam -> mr

Because the "general" option assumes minimal information from the input, the number of

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unclear about walt bam -> mr

Because the "general" option assumes minimal information from the input, the number of

8/31/17

FIDES LAY, … Fides Lay3

8/30/17

methcounts -c error

Thanks for the suggestion -- I found that the first ~80000 lines were null --deleting these lines

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methcounts -c error

Thanks for the suggestion -- I found that the first ~80000 lines were null --deleting these lines

8/30/17

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