MACS: peak calling from snATAC data
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`
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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?
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!
When constructing a file path in windows you either need to use either:
The
file.pathfunction (preferred)Two backslashes as separators.
Or single forward slahes.
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.
I did not create that path. It is automatically showing like that! How do I fix it!
Edit your question and include the code you ran before this to make the
visobject.I have updated it now.
Since you modified the code in the vignette to run your data, you need to include your code in the post.
But it's quiet big! If I include that then my main question will get buried!