MACS: peak calling from snATAC data
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12 weeks ago

Hi,

I followed this tutorial to create the object Vis (https://satijalab.org/signac/articles/pbmc_vignette.html). From the object created here, I have been trying the peak calling from signac package for my snATAC data. I keep running into this error. Can someone please tell me how to fix this!

CODE

peaks <- CallPeaks(

  object = vis,

  group.by = "seurat_clusters",

  macs2.path = "/usr/local/apps/python-packages/3.7.3/macs2/2.2.7.1/bin/macs2")

ERROR

Processing file \PROJECTS\outs\fragments.tsv.gz

Keeping 2563 cell barcodes

Splitting into 13 files

Done Processing 102 million lines  


    Error in file(file, "rt") : cannot open the connection
    In addition: Warning message:
    In file(file, "rt") :
    cannot open file 'C:\Users\AppData\Local\Temp\Rtmp04ptdN/0_peaks.narrowPeak': No such file or directory`
ATAC MACS Rstudio Peakcalling • 495 views
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It's showing both forward and back slashes in your file path, which is probably not correct. What OS are you doing this on?

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I am working in Windows. I also checked the path mentioned in the error. There is no such file there. But I am not how to get that file. I have run all the previous steps mentioned in the tutorial. I assume this file should automatically be there!

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When constructing a file path in windows you either need to use either:

The file.path function (preferred)

file.path("C:", "Users", "AppData", ...) 

Two backslashes as separators.

"C:\\Users\\AppData\\..."

Or single forward slahes.

"C:/Users/AppData/..."

If the file isn't there you should edit your post with the code you ran leading up to this step, otherwise we won't be able to help.

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I did not create that path. It is automatically showing like that! How do I fix it!

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Edit your question and include the code you ran before this to make the vis object.

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I have updated it now.

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Since you modified the code in the vignette to run your data, you need to include your code in the post.

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But it's quiet big! If I include that then my main question will get buried!

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