DANPOS

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sdhur...@gmail.com, simon holzinger2

Feb 20

error in running danpos3_MNase-seq

Hi Dhurjhoti, I fixed this bugs quite some time ago, unfortunately the maintainer of the GitHub repo

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error in running danpos3_MNase-seq

Hi Dhurjhoti, I fixed this bugs quite some time ago, unfortunately the maintainer of the GitHub repo

Feb 20

Maciej Kotliński, simon holzinger4

10/19/23

OverflowError: cannot convert float infinity to integer

Hi, the unexpected behaviour from diff is, because it is actually not the difference but the log10(

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OverflowError: cannot convert float infinity to integer

Hi, the unexpected behaviour from diff is, because it is actually not the difference but the log10(

10/19/23

Gilles Siréta, simon holzinger2

10/13/23

dpos ChiP-seq input, spike-in, replicates

Hi Gilles, First I am not the original developer of the program and although I used it a lot and went

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dpos ChiP-seq input, spike-in, replicates

Hi Gilles, First I am not the original developer of the program and although I used it a lot and went

10/13/23

Maciej Kotliński, simon holzinger3

10/13/23

AttributeError: 'numpy.float64' object has no attribute 'split' while runnink dpeak

Hi Maciek, sorry for not coming back to you earlier. Thanks for finding (and fixing) the bug. I never

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AttributeError: 'numpy.float64' object has no attribute 'split' while runnink dpeak

Hi Maciek, sorry for not coming back to you earlier. Thanks for finding (and fixing) the bug. I never

10/13/23

Adrià Mitjavila

7/4/23

DANPOS Profile not working

Dear Samantha, Thank you for the update of DANPOS to DANPOS3. I have been running DANPOS to calculate

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DANPOS Profile not working

Dear Samantha, Thank you for the update of DANPOS to DANPOS3. I have been running DANPOS to calculate

7/4/23

ly Andy, subhashini...@gmail.com2

7/3/23

about the results

Dear Andy, We had used DANPOS3 a few months back and had run both the dpos and dtriple functions. We

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about the results

Dear Andy, We had used DANPOS3 a few months back and had run both the dpos and dtriple functions. We

7/3/23

ly Andy, simon holzinger5

6/16/23

ValueError: connot convert float NaN to integer

Dear Simon, Can you help me to fix this problem? I have been unable to solve this problem. Best, Andy

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ValueError: connot convert float NaN to integer

Dear Simon, Can you help me to fix this problem? I have been unable to solve this problem. Best, Andy

6/16/23

5/23/23

Hi All, Are the older versions of the software no longer usable ? I have encountered many issues with

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Hi All, Are the older versions of the software no longer usable ? I have encountered many issues with

5/23/23

ly Andy, … simon holzinger4

5/17/23

TypeError: ppois() got an unexpected keyword argument 'lower_tail'

The fixed version is available in my current develop branch if you don't want to change the stuff

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TypeError: ppois() got an unexpected keyword argument 'lower_tail'

The fixed version is available in my current develop branch if you don't want to change the stuff

5/17/23

ly Andy, simon holzinger3

5/13/23

download the test data

Dear Simon, Thanks very much for you friendly. It my honor that you can provide the MNase dataset. My

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download the test data

Dear Simon, Thanks very much for you friendly. It my honor that you can provide the MNase dataset. My

5/13/23

Elisheva Heilbrun, simon holzinger2

4/21/23

Using DANPOS2 to determine nucleosome positions

Hi, Danpos can't handle bigwig files, so you have to convert the bigwig files to wig files first.

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Using DANPOS2 to determine nucleosome positions

Hi, Danpos can't handle bigwig files, so you have to convert the bigwig files to wig files first.

4/21/23

黄营长, … yashoda....@gmail.com12

11/30/22

ValueError: math domain error

Hello, I am posting here a solution to the math domain error related to pf and ppois functions in

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ValueError: math domain error

Hello, I am posting here a solution to the math domain error related to pf and ppois functions in

11/30/22

Galleria Alternativa, NP2

9/23/22

DANPOS3 installation problem

Hi, I'm no pro on this but it could be that you need to specify "python" before "

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DANPOS3 installation problem

Hi, I'm no pro on this but it could be that you need to specify "python" before "

9/23/22

9/23/22

interpreting height_logP

Hi, I ran successfully dtriple and in the .peaks output I can't really comprehend the values I

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interpreting height_logP

Hi, I ran successfully dtriple and in the .peaks output I can't really comprehend the values I

9/23/22

Alex Chen, … NP4

9/23/22

IndexError: list index out of range

I removed the mitochondrion from bed input and it worked... Le vendredi 23 septembre 2022 à 14:00:09

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IndexError: list index out of range

I removed the mitochondrion from bed input and it worked... Le vendredi 23 septembre 2022 à 14:00:09

9/23/22

hang zhao, simon holzinger2

9/23/22

Dynamic nucleosome identification

Hi Hang, I don't know if I can help you, but there are several things worth mentioning: The

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Dynamic nucleosome identification

Hi Hang, I don't know if I can help you, but there are several things worth mentioning: The

9/23/22

7/13/21

KeyError: '211000022278074'

I'm running the dpos function on a set of paired control/treatments with their respective inputs.

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KeyError: '211000022278074'

I'm running the dpos function on a set of paired control/treatments with their respective inputs.

7/13/21

David Castillo Rodríguez, sjk...@gmail.com5

3/29/21

TypeError: 'numpy.float64' object cannot be interpreted as an integer

Hello Sammy, happy to help. Unfortunately, soon after, I stumbled into a new problem: https://groups.

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TypeError: 'numpy.float64' object cannot be interpreted as an integer

Hello Sammy, happy to help. Unfortunately, soon after, I stumbled into a new problem: https://groups.

3/29/21

Monica B, David Castillo Rodríguez3

3/28/21

Issues: How much computing power? And parsing from Bam file question.

I was getting similar logs as you, regarding this: parsing from Bam file ... I then added the --

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Issues: How much computing power? And parsing from Bam file question.

I was getting similar logs as you, regarding this: parsing from Bam file ... I then added the --

3/28/21

11/24/20

Under what license is DANPOS distributed? Thanks, Jim

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Under what license is DANPOS distributed? Thanks, Jim

11/24/20

10/20/20

DANPOS3 runs but does not save?-- please help

Hello, I am trying to run danpos3 dpos on a series of .bam files. These bam files have paired end

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DANPOS3 runs but does not save?-- please help

Hello, I am trying to run danpos3 dpos on a series of .bam files. These bam files have paired end

10/20/20

libin...@gmail.com

9/24/20

DANPOS3 wiq does not work

Hi I am trying to normalise my replicates with quantile normalisation but the wig.py seems does not

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DANPOS3 wiq does not work

Hi I am trying to normalise my replicates with quantile normalisation but the wig.py seems does not

9/24/20

Bn Li, Sammy Klasfeld2

8/6/20

DANPOS3 does not work with paired end bam file or bed file

Thank you so much for reporting this error. Try pulling the repository again. I think I fixed the bug

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DANPOS3 does not work with paired end bam file or bed file

Thank you so much for reporting this error. Try pulling the repository again. I think I fixed the bug

8/6/20

Eric Wright, … Sammy Klasfeld14

7/19/20

dtriple error in "danpos3" TypeError: 'float' object cannot be interpreted as an integer

I rolled my system back from Ubuntu 20.04 to 18.04 and it doesn't totally lock up when running

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dtriple error in "danpos3" TypeError: 'float' object cannot be interpreted as an integer

I rolled my system back from Ubuntu 20.04 to 18.04 and it doesn't totally lock up when running

7/19/20

7/10/20

dtriple negative fragment sizes with paird-end input

Hello, I have two replicates for K27me3 generated by CUT&RUN sequenced by paired-end. From the

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dtriple negative fragment sizes with paird-end input

Hello, I have two replicates for K27me3 generated by CUT&RUN sequenced by paired-end. From the

7/10/20

Sammy Klasfeld, Kaifu Chen3

6/30/20

I Updated Danpos2 to Danpos3

Hello Kaifu, Thank you so much for the quick response. It would be great if you could post my version

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I Updated Danpos2 to Danpos3

Hello Kaifu, Thank you so much for the quick response. It would be great if you could post my version

6/30/20

javier...@gmail.com, Sammy Klasfeld3

6/24/20

Problems with rpy2 installing danpos2

I edited the current script to work with updated versions of R and python. https://github.com/

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Problems with rpy2 installing danpos2

I edited the current script to work with updated versions of R and python. https://github.com/

6/24/20

Rita CC, Saurabh Chaudhary2

5/16/20

docker error about robject.py

Hi! Rita, I am not an expert in programming. But I think you need to reinstall the upgraded version

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docker error about robject.py

Hi! Rita, I am not an expert in programming. But I think you need to reinstall the upgraded version

5/16/20

Chester Lee, Alex Ranieri6

12/12/19

p-value cut-off for nuclsosome calling

Nice! Em quarta-feira, 11 de dezembro de 2019 23:11:15 UTC-3, Chester Lee escreveu: It works! Thank

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p-value cut-off for nuclsosome calling

Nice! Em quarta-feira, 11 de dezembro de 2019 23:11:15 UTC-3, Chester Lee escreveu: It works! Thank

12/12/19

Saurabh Chaudhary, Alex Ranieri2

11/18/19

error in --fdr function

Hi. I think there is a similar error that was resolved here: https://groups.google.com/forum/#!topic/

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error in --fdr function

Hi. I think there is a similar error that was resolved here: https://groups.google.com/forum/#!topic/

11/18/19

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