This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to install bedClip on a Mac Book Pro?

I would like to run bedClip to trim peaks called by MACS that are longer than the chromosome size. I have downloaded bedClip from UCSC (http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/bedClip). However, it doesn't work when I run some commands like: bedClip input.bed mm9 output.bed (followed direction of http://biofeed.tumblr.com/post/16758640444/ngschip-seq-bedclip-to-clip-out-off-end). I think the problem is that I don't know how to properly install bedClip on my Mac Book Pro using Terminal. I also found three posts about bedClip on BioStar, but no one said how to install the bedClip. Anyone can help me? Thank you very much.

bedclip chip-seq ucsc macs
• 3,205 views • link
updated by Ram Ram • written by Gary Gary

However, it doesn't work when I run some commands

What's the problem?

• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

The terminal show that: -bash: bedClip: command not found

• 0 views • link
updated by Ram Ram • written by Gary Gary

Hello Gary!

We believe that this post does not fit the main topic of this site.

Not related to bioinformatics. Just a basic PATH problem.http://www.linuxnix.com/2012/07/how-to-set-path-in-linux-and-unix.html

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Hi Pierre,

In fact, I am a newer of unix command lines. Many thanks for your information. I can run the bedClip now.

• 0 views • link
updated by Ram Ram • written by Gary Gary

0 answers

No answers yet.

Log in to answer this question.

More posts like this