makeBigWig.pl

yueli · 06-30-2019, 03:35 PM

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

colindaven · 07-01-2019, 03:52 AM

The error says it all "could not find bedGraphToBigWig".

Have a read about Linux and PATH and and or install/configure this program properly in your PATH.

Else try deeptools via bioconda, it's likely to work better.

yueli · 07-01-2019, 04:48 PM

Hello, Colindaven,

Thank you so much for your great help!

Best,

Yue

06-30-2019, 03:35 PM	#1
yueli Member Location: china Join Date: May 2013 Posts: 71	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

07-01-2019, 03:52 AM	#2
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 417	The error says it all "could not find bedGraphToBigWig". Have a read about Linux and PATH and and or install/configure this program properly in your PATH. Else try deeptools via bioconda, it's likely to work better.

07-01-2019, 04:48 PM	#3
yueli Member Location: china Join Date: May 2013 Posts: 71	Hello, Colindaven, Thank you so much for your great help! Best, Yue