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karmel / homer-idr

Applying IDR analysis to Homer peaks.
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bug in: 8. Call peaks on each of the pooled pseudoreplicate tag directories. #2

Closed xflicsu closed 8 years ago

xflicsu commented 9 years ago

Hello, I use homer-idr to do idr analysis with the step as the readme shown to me. And I find that there is no directory named "pseudoreps/pooled-pseudoreps" in step 8. So, is there any other commands to produce files in that directory? Thanks!

karmel commented 9 years ago

Yes-- in the beginning of that step, you create the directory with the mkdir command:

cd ~/CD4TCell-IDR
mkdir -p peaks/pooled-pseudoreps
cd peaks/pooled-pseudoreps

Does that help?

xflicsu commented 9 years ago

Sorry for the misleading words! I mean there is no input directory named "pseudoreps/pooled-pseudoreps" (but not "peaks/pooled-pseudoreps") in the below command.

########################### for f in ~/CD4TCell-IDR/pseudoreps/pooled-pseudoreps/* .............. ###########################

And I checked step 5 and step 6. Only two directory, "pseudoreps/individual" and "pseudoreps/pooled", were created. So, when and how to create directory named "pseudoreps/pooled-pseudoreps" to prepare for input of step 8?

karmel commented 9 years ago

Ah, sorry for misreading-- that's a typo in the instructions, and should be 

for f in ~/CD4TCell-IDR/pseudoreps/pooled/*

which was created in step 6. I will update the text-- thanks!