th usage of makebigwig.pl

Question

[yueli7]

Hello, I

I tried to use makeBigWig.pl

Acutally, bedGraphToBigWig has installed.

Thanks for any help!

Yue

administrator@ACB-HuangLab-Ubuntu:~/homer_01/bin$ perl makeBigWig.pl PU.1-ChIP-Seq/ mm9  -webDir /var/www/bigWigs/ -url http://ChuckNorrisU.edu/bigWigs

!!! Could not detect bedGraphToBigWig program in the executable path !!!
    Download it from http://hgdownload.cse.ucsc.edu/admin/exe/

administrator@ACB-HuangLab-Ubuntu:~/homer_01/bin$ ./bedGraphToBigWig
bedGraphToBigWig v 4 - Convert a bedGraph file to bigWig format.
usage:
bedGraphToBigWig in.bedGraph chrom.sizes out.bw

Answer 1

[Ram]

The error message is clear: bedGraphToBigWig is not in $PATH. Try running:

PATH=$PATH:~/homer_01/bin perl makeBigWig.pl PU.1-ChIP-Seq/ mm9  -webDir /var/www/bigWigs/ -url http://ChuckNorrisU.edu/bigWigs

Or add the location to your path using:

echo 'export PATH=$PATH:~/homer_01/bin' >>~/.bash_profile
source ~/.bash_profile

and then you can run your first command and it will just work.

[yueli7]

Hello, RamRs,

Thank you so much for your great help!

Thank you again!

Yue

[Ram]

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