error at pcatype=cis level

[Sen0108]

I encountered "Performing block wise correlation calculation Error: upper value must be greater than lower value" this error. Please suggest. I have tried 50K,100K, 1MB resolution.

[ay-lab]

Please check the input you're providing.
dcHiC accepts a three-column hic interaction file like the following -

1 2 10
1 3 8
..

The first two columns are the indices of the genomic region provided in the bed file, and the third column represents the interaction count.

The first column index must be less than or equal to the second column index number. If it is not than it will raise the error.

[Sen0108]

yeah basic the .matrix file from hicpro output. right?

[ay-lab]

Yes

[Sen0108]

I tried your suggestion. However it is still showing errors.
if using --ebackgrnd=2
Error in aggregate.data.frame(lhs, mf[-1L], FUN = FUN, ...) :
no rows to aggregate
Calls: lapply ... aggregate -> aggregate.formula -> aggregate.data.frame
if using --ebackgrnd=1
Performing block wise correlation calculation Error: upper value must be greater than lower value
error

[ay-lab]

Can you just check this awk '$1 > $2 { print }' <matrix file> |wc -l

[Sen0108]

Tried that and modified the matrix file as per your last instructions.

[ay-lab]

Great! Let me know if you face any other issues.