Re^3: could not open configuration file

$ perl configureHomer.pl -bigWigDir

I'm pretty sure that's not how you're supposed to use it, according to the documentation and the soruce, -bigWigDir should be followed by a new URL. You're getting the "Use of uninitialized value" warning because of the missing argument. But why run this command at all - maybe just try using the default settings first?

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Re^4: could not open configuration file by yueli711 (Sexton) on Jun 30, 2019 at 17:02 UTC
Hello, haukex, Thank you so much for your response. I tried to use makeBigWig.pl to transfer thefile to bigwig and I can visualize it in UCSC browser. Following is the protocol. Thank you again for your great help! Yue Li `To make bigWig files easier to generate, HOMER includes a program crea +tively named "makeBigWig.pl" that automates all of the steps below. makeBigWig.pl <tag directory> <genome> [special options] [makeUCSC fil +e options] -webDir /path-to-web-fold/ -url http://webserverURL/bigwig +Fold/ i.e. makeBigWig.pl PU.1-ChIP-Seq/ mm9 -webDir /var/www/bigWigs/ -url +http://ChuckNorrisU.edu/bigWigs/` [download]	[reply] [d/l]

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Re^4: could not open configuration file
by yueli711 (Sexton) on Jun 30, 2019 at 17:02 UTC

Hello, haukex, Thank you so much for your response. I tried to use makeBigWig.pl to transfer thefile to bigwig and I can visualize it in UCSC browser. Following is the protocol. Thank you again for your great help! Yue Li

To make bigWig files easier to generate, HOMER includes a program crea
+tively named "makeBigWig.pl" that automates all of the steps below.

makeBigWig.pl <tag directory> <genome> [special options] [makeUCSC fil
+e options] -webDir /path-to-web-fold/ -url http://webserverURL/bigwig
+Fold/
i.e. makeBigWig.pl PU.1-ChIP-Seq/ mm9  -webDir /var/www/bigWigs/ -url 
+http://ChuckNorrisU.edu/bigWigs/
[download]

[reply]
[d/l]