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:
- Preparing the appropriate input data.
- Running the analysis.
2 answers
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.
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
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~
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).
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")
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