Tutorial:Determine if a transcription factor is bound with CENTIPEDE

Question

[Kamil]

I wrote a practical tutorial for how to use CENTIPEDE to determine if a transcription factor is bound to a site in the genome.

The tutorial provides step-by-step instructions for:

1. Preparing the appropriate input data.
2. Running the analysis.

Answer 1

[chadi.elfarran]

Hi Kamil,

Thank you for producing this great tutorial.

I have a question. When I try to use the centipede_data function of the R package that you have provided, I always end up getting this error:

Error in sprintf("%.bai", bam_file) :
  invalid format '%.ba'; use format %s for character objects

Do you have any suggestion to solve this issue?

Thanks a lot.

[Kamil]

Thanks for catching the error, now fixed.

[chadi.elfarran]

Works perfectly.

Thank you once again for the effort to produce this great package. You have made it very easy to use CENTIPEDE.

Best Regards,

Chadi

Answer 2

[wujiaqi]

Hi Kamil,

Thank you again for producing this fantastic tutorial.

When I use devtools::install_github("slowkow/CENTIPEDE.tutorial") to install the tutorial, I got this error:

Downloading GitHub repo slowkow/CENTIPEDE.tutorial@master
Error in curl::curl_fetch_memory(url, handle = handle) :
  couldn't resolve host name

Could you please help me with this problem? I searched it in many websites but still no answer.

Thank you. And early to wish you Merry Christmas and Happy New Year~

[Sam]

Are you working behind a university computer? If you are you'll probably need to set up a proxy to avoid the error.

library(httr)
set_config(use_proxy(url="proxy.xxxx.com", port=xxxx, username="user",password="password"))

Only fill in the username and password field if you need a username and password to use the proxy. Make sure you also have devtools and Rtools installed (can be installed via the install.packages("") function).

[Kamil]

This worked for me. First, download a ZIP archive of the github repository: https://github.com/slowkow/CENTIPEDE.tutorial/archive/master.zip

Next, run these commands in R:

install.packages("git2r")
devtools::install_local("~/Downloads/CENTIPEDE.tutorial-master.zip")

[wujiaqi]

Thank you a lot.

I got this error:

package 'git2r' is not available (for R version 3.2.2)

Should I use the 2.* version?

[Kamil]

Please see this thread for more help on installing packages in R:

https://stackoverflow.com/questions/25721884/how-should-i-deal-with-package-xxx-is-not-available-for-r-version-x-y-z-wa