th usage of makebigwig.pl

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

chip-seq

• 1,850 views • link

updated 7.1 years ago by Ram

• written 7.1 years ago by yueli7

1 answer

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.

• 0 views • link

written 7.1 years ago by Ram

Hello, RamRs,

Thank you so much for your great help!

Thank you again!

Yue

• 0 views • link

written 7.1 years ago by yueli7

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work.

• 0 views • link

written 7.1 years ago by Ram