ying-w / chipseq-compare Goto Github PK

Hi @ying-w

I'm thanking you for MAnorm improvement!!!!!! You made my day!

But, please, could you explain me the meaning of files gr_peak.bed and er_peak.bed in MAnorm3.sh?
I have the following files for each condition:

• replicate1
• replicate2
• control for replicate1
• control for replicate2

And I need to compare two such conditions, but stuck in choosing gr_peak and er_peak. How can I get this files?

Sorry, this is not my major and I'm learning.

Thank you a lot for the answer, Sergey

I am facing following issue while running MAnorm3.R

ls: cannot access './chk/*xls': No such file or directory
../MAnorm3.sh: 414: ../MAnorm3.sh: [[: not found
MAnorm3.R did not create excel output file check chk_Rcommand.out
no excel file is generated , any idea why?

Hi, I've been working on a project that explores different binding patterns in intestine and kidney tissue. Your method, MAnorm3, is one of several methods that am using for my research. However, I seem to be running into this error of it not being able to open the excel file/it doesn't exist.

This is everything if the error output file:
ls: cannot access ./BB4_Int_Kid/*xls: No such file or directory
srun: error: hal0037: task 0: Exited with exit code 1

Thanks
S. Luo

I have a question regarding results of MAnorm , the result contains following header :
chr start end description #raw_read_1 #raw_read_2 M_value_rescaled A_value_rescaled -log10(p-value)

I want to know the detail about column raw_read1 & raw_read2 , what does it refers to?