bigWigAverageOverBed

[Per Wahlberg]

Hi!

I am trying to use the bigWigAverageOverBed program, it works fine in default settings but not if I apply the "-bedOut=out.bed" option to write the original bed with mean column appended. I don't get an error message but it prints out the usage options.

Is there something obvious that I am missing ?

here is my command:
bigWigAverageOverBed hg19.phyloP.bw 1kbWin_shuf1000_size.bed -bedOut=out.bed

Any suggestion most welcome.

regards,

Per

[Brian Lee]

Dear Per,

Thank you for using the UCSC Genome Browser and your question about the bigWigAverageOverBed utility.

Your command is missing the final argument, even though you are specifying out.bed, you still need something like "out.tab" specified:

usage:   bigWigAverageOverBed in.bw in.bed out.tab

--->

bigWigAverageOverBed hg19.phyloP.bw 1kbWin_shuf1000_size.bed -bedOut=out.bed out.tab

You will then find two files created. The desired out.bed, and the required specified out.tab:

chr10 69644939 69678147 SIRT1 1.49176

SIRT1 33208 2487 3710 0.11172 1.49176

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UCSC Genome Bioinformatics Group

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