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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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Error in step 2 of the run_dchic.sh script #72

Open asgda opened 1 year ago

asgda commented 1 year ago 
Error in aggregate.data.frame(lhs, mf[-1L], FUN = FUN, ...) : 
  no rows to aggregate
Calls: pcselect ... aggregate -> aggregate.formula -> aggregate.data.frame
In addition: Warning message:
In cor(cbind(chrom.list[[j]], tss = pca$tss)) :
  the standard deviation is zero
Execution halted

GOT THE ABOVE ERROR WHILE RUNNING STEP2 USING THE FOLLOWING COMMAND: Rscript dchicf.r --file input.txt --pcatype select --dirovwt T --genome hg38

I have checked that the locations are absolutely fine for each file and the genome is hg38. Also, the step 1 command gave out proper results without any errors, i.e., it created the folders with all the experiments.

Any way of resolving this error? Any help is appreciated.

ay-lab commented 1 year ago

For what Hi-C resolution are you running the compartment analysis?

asgda commented 12 months ago

The resolution is 10000 which we are using.

ay-lab commented 12 months ago

To ensure there is no issue with the downloaded hg38 files, can you please run the analysis at 100Kb resolution? Also, is there any non-standard chromosome in the analysis?

asgda commented 11 months ago

We have Y chromosome in it. Now, we will try with 100 kb resolution and see what is the output.

Sen0108 commented 3 months ago

I have encountered same issue.. I have tried with 100kb. Didn't work

Sen0108 commented 3 months ago

find a way... try to utilize eBackgroud scheme 1