Questions regarding running dcHiC about dchic HOT 7 CLOSED

Hi,

Thanks for trying out the package. It seems like you don't have the 'parallel' R package. If not, then please install it from here https://cran.r-project.org/web/packages/parallelly/index.html or type install.packages('parallel') within the R environment. I hope this will resolve the first issue.

Regarding the second issue, please install the 'bedtools' package from here https://bedtools.readthedocs.io/en/latest/ and please make sure the tool is in your $PATH. This is a must package to have for dchic.

I hope the rest of the issues will be resolved once you follow the above instructions.

from dchic.

Hi Ay,

Thanks for your reply! I actually have the parallel package installed in R, and I asked for help from the HPC staff of our university for installing bedtools. It is now installed, and I can load it, and call it, but the error message is still there. Do you have any other advice?

Thanks!

from dchic.

Hi,

You can try out two options - first, you can run with '--cthread 1 --pthread 1' option, so that you will avoid using the clusterApply part. The second option is to log into your HPC system in interactive mode and run dchic with '--cthread 2 --pthread 2' option. Let's try to resolve this issue, I can then help you to resolve the next.

from dchic.

Thank you, Ay. I tried the first option, and I got a new error, "Performing Z transformation : complete!
Performing block wise correlation calculation Error in functionsdchic::oe2cor(mat, (start - 1), (end - 1), 1, 0) :
upper value must be greater than lower value
Calls: lapply -> FUN -> lapply -> FUN ->
Execution halted".

from dchic.

Thanks for trying out the option. It seems like an issue either with the file format or the presence of a non-conventional chromosome with very few counts. Do you mind sending me the input bed file and a slice of the matrix files to [email protected]?

from dchic.

Thank you, Ay, for this kind suggestion! However, because this is unpublished data yet, we may need some time to think about it.

from dchic.

An alternative option is to run the PCA calculation separately (using HOMER/juicer) and use dcHiC to call the differential compartments. Please check the "Using Existing PC values with dcHiC" option under the utility folder.

from dchic.