"webdir" must be set to something

Question

[yueli7]

Hello,

I tried to demonstrate the example of makBIgWig.pl in homer package.

Thanks in advance for great help.

Best,

Yue

administrator@ACB-HuangLab-Ubuntu:~/homer_01/bin$ PATH=$PATH:~/homer_01/bin perl makeBigWig.pl PU.1-ChIP-Seq/ mm9  -webDir /var/www/bigWigs/ -url http://ChuckNorrisU.edu/bigWigs
!!! "-webdir" must be set to something (can also modify config.txt file)

[ATpoint]

yueli7, there is no point in posting every error message while trying to get this script to work. Google the errors. From the homer website

 -webdir <directory> (name of directory to place resulting bigWig file)

You have to set this option to tell the tool where to put the output. In your command it is webDir, not webdir. Please be smart and check your commands extensively, use google, before posting.

by the way, taking over these funny dummy commands (chucknorris) will not get you anywhere...

[yueli7]

Thanks you so much!

I was totally confusing of these days.

Thank you again.

Yue

Answer 1

[ATpoint]

You seem to be in quite some trouble with this script. Why don't you simply use bamCoverage from deeptools and view the resulting bigwig file on the Integrated Genome Viewer (IGV)? That is far simpler than using this homer script. It only requires an indexed BAM file.

[yueli7]

Thank you again for your suggestion.

[yueli7]

Hello, ATpoint,

Thank you again for your great help!

When I input the tmp.bw file into IGV, it said:

Thank you again!

Best,

Yue

administrator@ACB-HuangLab-Ubuntu:~/anaconda3/bin$ ./bamCoverage -b control_marked_duplicates.bam  -o   tmp.bw --outFileFormat bedgraph


Error loading /home/administrator/anaconda3/bin/tmp.bw: Error reading BBFile header for: /home/administrator/anaconda3/bin/tmp.bw

[ATpoint]

You want to make a bigwig, why did you set output to bedGraph? Leave this option at default to get a bigwig.

[yueli7]

Hello, ATpoint,

Thank you so much for your great help!

It works!

Thank you again!

Best,

Yue