Unable to use bedClip function
Peters, F.S. (Fleur)
Dear madam/sir,
I am writing you to try and figure out why I haven't succeeded in running bedClip.
I am running an ATACseq pipeline in which I am supposed to run bedClip. My programming is in the command line of a linux shell within windows. I have tried to install bedClip through various ways but I still get the error: bedClip: command not found.
I have tried installing the whole kent tools package by cloning the github. I also tried to install bedClip individually. I see the file in my directory and installing doesn't give error or warning but It still says bedClip: command not found. Is there an extra step that I am missing why it doesn't recognize it as a command? Below I have specified the commands I've used to install and how I would like to run bedClip.
slopBed -i "${input}"_FE.bdg -g "$chrsz" -b 0 | bedClip stdin "$chrsz" "${output}"
It would we wonderful if you can help me solve this issue. Thanks in advance.
Best wishes,
Fleur Peters
Fleur S. Peters PhD | Postdoctoral Researcher
Immuno-Hematology | Dept. of Experimental Immunology
Location AMC | K0-154 | Meibergdreef 9, 1105 AZ Amsterdam
T: 020 566 7688 | E: f.s.p...@amc.uva.nl
www.amsterdamumc.nl
| www.amc.nl
VUmc disclaimer : www.vumc.nl/disclaimer
AMC disclaimer : www.amc.nl/disclaimer
Daniel Schmelter
Hello Fleur,
Thank you for using the Genome Browser and for your question about using our command-line utilities.
It looks like you may not have enabled permission to execute that command using "chmod". Furthermore, unless configured otherwise, you probably need to specify the exact path of the bedClop program when you run it. Brief instructions are available in the utilities section here:
http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads
Just to make it absolutely clear, here are the commands for your application with the full paths specified:
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedClip
chmod +x ./bedClip
slopBed -i "${input}"_FE.bdg -g "$chrsz" -b 0 | ./bedClip stdin "$chrsz" "${output}"
We hope this is helpful. If there is any further problems, please let us know. Reply-all to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, please reply-all to genom...@soe.ucsc.edu.
All the best,
Daniel Schmelter
UCSC Genome Browser
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