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guanjue / IDEAS_2018

Jointly characterizing epigenetic dynamics across multiple cell types
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Imputation files #8

Closed Lila14 closed 5 years ago

Lila14 commented 5 years ago

Where are the output files for imputed chromatin marks?

yuzhang123 commented 5 years ago

No marks are imputed by default.

----- Original Message ----- From: Lila Rieber notifications@github.com To: guanjue/IDEAS_2018 IDEAS_2018@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Sent: Fri, 19 Oct 2018 17:01:40 -0400 (EDT) Subject: [guanjue/IDEAS_2018] Imputation files (#8)

Where are the output files for imputed chromatin marks?

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Lila14 commented 5 years ago

Alright but if I set the parameters file to impute certain marks, where will the output files be?

On Fri, Oct 19, 2018 at 5:23 PM Yu Zhang notifications@github.com wrote:

No marks are imputed by default.

----- Original Message ----- From: Lila Rieber notifications@github.com To: guanjue/IDEAS_2018 IDEAS_2018@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Sent: Fri, 19 Oct 2018 17:01:40 -0400 (EDT) Subject: [guanjue/IDEAS_2018] Imputation files (#8)

Where are the output files for imputed chromatin marks?

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yuzhang123 commented 5 years ago

It should be in the same folder as state files. ----- Original Message ----- From: Lila Rieber notifications@github.com To: guanjue/IDEAS_2018 IDEAS_2018@noreply.github.com Cc: Yu Zhang yzz2@psu.edu, Comment comment@noreply.github.com Sent: Fri, 19 Oct 2018 17:24:22 -0400 (EDT) Subject: Re: [guanjue/IDEAS_2018] Imputation files (#8)

Alright but if I set the parameters file to impute certain marks, where will the output files be?

On Fri, Oct 19, 2018 at 5:23 PM Yu Zhang notifications@github.com wrote:

No marks are imputed by default.

----- Original Message ----- From: Lila Rieber notifications@github.com To: guanjue/IDEAS_2018 IDEAS_2018@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Sent: Fri, 19 Oct 2018 17:01:40 -0400 (EDT) Subject: [guanjue/IDEAS_2018] Imputation files (#8)

Where are the output files for imputed chromatin marks?

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Lila14 commented 5 years ago

How will the files be named?

On Fri, Oct 19, 2018 at 5:26 PM Yu Zhang notifications@github.com wrote:

It should be in the same folder as state files. ----- Original Message ----- From: Lila Rieber notifications@github.com To: guanjue/IDEAS_2018 IDEAS_2018@noreply.github.com Cc: Yu Zhang yzz2@psu.edu, Comment comment@noreply.github.com Sent: Fri, 19 Oct 2018 17:24:22 -0400 (EDT) Subject: Re: [guanjue/IDEAS_2018] Imputation files (#8)

Alright but if I set the parameters file to impute certain marks, where will the output files be?

On Fri, Oct 19, 2018 at 5:23 PM Yu Zhang notifications@github.com wrote:

No marks are imputed by default.

----- Original Message ----- From: Lila Rieber notifications@github.com To: guanjue/IDEAS_2018 IDEAS_2018@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Sent: Fri, 19 Oct 2018 17:01:40 -0400 (EDT) Subject: [guanjue/IDEAS_2018] Imputation files (#8)

Where are the output files for imputed chromatin marks?

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yuzhang123 commented 5 years ago

It should have the mark name and cell name in the file name. If you can’t find it, probably I didn’t implement in the runme script.

----- Original Message ----- From: Lila Rieber notifications@github.com To: guanjue/IDEAS_2018 IDEAS_2018@noreply.github.com Cc: Yu Zhang yzz2@psu.edu, Comment comment@noreply.github.com Sent: Fri, 19 Oct 2018 17:36:31 -0400 (EDT) Subject: Re: [guanjue/IDEAS_2018] Imputation files (#8)

How will the files be named?

On Fri, Oct 19, 2018 at 5:26 PM Yu Zhang notifications@github.com wrote:

It should be in the same folder as state files. ----- Original Message ----- From: Lila Rieber notifications@github.com To: guanjue/IDEAS_2018 IDEAS_2018@noreply.github.com Cc: Yu Zhang yzz2@psu.edu, Comment comment@noreply.github.com Sent: Fri, 19 Oct 2018 17:24:22 -0400 (EDT) Subject: Re: [guanjue/IDEAS_2018] Imputation files (#8)

Alright but if I set the parameters file to impute certain marks, where will the output files be?

On Fri, Oct 19, 2018 at 5:23 PM Yu Zhang notifications@github.com wrote:

No marks are imputed by default.

----- Original Message ----- From: Lila Rieber notifications@github.com To: guanjue/IDEAS_2018 IDEAS_2018@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Sent: Fri, 19 Oct 2018 17:01:40 -0400 (EDT) Subject: [guanjue/IDEAS_2018] Imputation files (#8)

Where are the output files for imputed chromatin marks?

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Lila14 commented 5 years ago

I've attached the files I used to run IDEAs (with the test data). The other files were defaults. I removed MEP h3k27ac from the input file so that it would impute. run_IDEAS.parafile.txt run_IDEAS.input.txt

yuzhang123 commented 5 years ago

Maybe it is a bug? what if you switch row 2 and row 3 in input.txt?

The output file name should include ".impute.h3k27ac." in either where you run the code or your specified output folder.

On 10/20/18 11:39 AM, Lila Rieber wrote:

I've attached the files I used to run IDEAs (with the test data). The other files were defaults. I removed MEP h3k27ac from the input file so that it would impute. run_IDEAS.parafile.txt https://github.com/guanjue/IDEAS_2018/files/2498288/run_IDEAS.parafile.txt run_IDEAS.input.txt https://github.com/guanjue/IDEAS_2018/files/2498289/run_IDEAS.input.txt

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Lila14 commented 5 years ago

This didn't work. Would you mind attaching an example of a working imputation?

guanjue commented 5 years ago

I have generated the results with imputation. The IDEAS can impute and save the missing data. The results are saved in the .gz files -rw-rw---- 1 gzx103 gzx103_collab 131K Oct 21 13:36 test_IDEAS.chr1.impute.ERY_ad.gz -rw-rw---- 1 gzx103 gzx103_collab 160K Oct 21 13:36 test_IDEAS.chr1.impute.MEP.gz -rw-rw---- 1 gzx103 gzx103_collab 181K Oct 21 13:36 test_IDEAS.chr1.impute.GMP.gz -rw-rw---- 1 gzx103 gzx103_collab 323K Oct 21 13:36 test_IDEAS.chr1.impute2.ERY_ad.gz -rw-rw---- 1 gzx103 gzx103_collab 595K Oct 21 13:36 test_IDEAS.chr1.impute2.MEP.gz -rw-rw---- 1 gzx103 gzx103_collab 321K Oct 21 13:36 test_IDEAS.chr1.impute2.GMP.gz

If some of your cell types have missing marks (after you removing the MEP h3k27ac from the input file), the IDEAS will impute the marks.

However, if all of your cell types have all marks, the IDEAS will not impute the marks.

Lila14 commented 5 years ago

Can you attach your input files?

On Sun, Oct 21, 2018 at 1:43 PM Guanjue Xiang notifications@github.com wrote:

I have generated the results with imputation. The IDEAS can impute and save the missing data. The results are saved in the .gz files -rw-rw---- 1 gzx103 gzx103_collab 131K Oct 21 13:36 test_IDEAS.chr1.impute.ERY_ad.gz -rw-rw---- 1 gzx103 gzx103_collab 160K Oct 21 13:36 test_IDEAS.chr1.impute.MEP.gz -rw-rw---- 1 gzx103 gzx103_collab 181K Oct 21 13:36 test_IDEAS.chr1.impute.GMP.gz -rw-rw---- 1 gzx103 gzx103_collab 323K Oct 21 13:36 test_IDEAS.chr1.impute2.ERY_ad.gz -rw-rw---- 1 gzx103 gzx103_collab 595K Oct 21 13:36 test_IDEAS.chr1.impute2.MEP.gz -rw-rw---- 1 gzx103 gzx103_collab 321K Oct 21 13:36 test_IDEAS.chr1.impute2.GMP.gz

If some of your cell types have missing marks (after you removing the MEP h3k27ac from the input file), the IDEAS will impute the marks.

However, if all of your cell types have all marks, the IDEAS will not impute the marks.

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guanjue commented 5 years ago

run_IDEAS_with_imputation.input.txt

guanjue commented 5 years ago

GMP.h3k4me3.1M.txt GMP.h3k27ac.1M.txt

These are the new input files

Lila14 commented 5 years ago

It's still not producing imputation files for me. Can you send a zip file of everything you ran? Also, I keep having to change the file paths because you're using paths specific to your system. It's unlikely that this is the issue, but it might be easier if you used relative paths.

guanjue commented 5 years ago

Here is the zip file of the folder I run it. I deleted the output state files because the uploading limitation of the file size. https://github.com/guanjue/IDEAS_2018/blob/master/test_data.zip

For the input file, it has to be the absolute paths. Otherwise, there output will not be generated.

Lila14 commented 5 years ago

I got it working now. I think the issue was that I had to set "impute= All", instead of "impute= h3k27ac" for example.