epigen / crop-seq Goto Github PK

Hello, I'm trying to recreate the plot in Figure 2B of your paper using the function screen_dynamics.py, but I can't find the input data in the supplementary files or at the GEO accession. Can you please point me towards it?

Thank you for putting all of your code online!

Hey
I am trying to run the whole pipeline for crop-seq, i am at the assign_gRNA_cells.py step and it is giving error.
File "assign_gRNA_cells.py", line 359, in
prj.add_sample_sheet()
File "crop-seq-final_version/src/looper/looper/models.py", line 546, in getattr
AttributeError: add_sample_sheet

Please let me know if you have any idea about the error

Thanks,
Kashish Chetal

Hello,
I'm trying to perform some test runs with your pipeline as soon i will have to do it on my own cropseq data. However i'm getting this error.

python src/guides_to_ref.py Traceback (most recent call last): File "src/guides_to_ref.py", line 3, in <module> from looper.models import Project ModuleNotFoundError: No module named 'looper.models' Makefile:7: recipe for target 'makeref' failed make: *** [makeref] Error 1
i have the latest version of looper where there is no project.py. However if i ignore the line i get this error.

python src/guides_to_ref.py Traceback (most recent call last): File "src/guides_to_ref.py", line 58, in <module> prj = Project(os.path.join("metadata", "config.yaml")) NameError: name 'Project' is not defined Makefile:7: recipe for target 'makeref' failed make: *** [makeref] Error 1
now i've tried using the older 0.7.2 version but there i get into some more issues and was hoping that there might be a simper solution from the start.
thank you in advance.

Regards,
Lucas Kuijpers
PhD student

Hi!
when i run this command 'make makeref' command, i got an error. Indeed,it caused by this
prj = Project(os.path.join("metadata", "config.yaml")),Could you help me! Moreover,in the config.yaml,what does the pipelines_dir refer to?Thanks!