I used HiC-Pro to generate BAM files and then the bam2chicago.sh script to get the chinput file. I then ran the runChicago.R wrapper and I get:
I'm getting the following output: Processing input...
Read 0.0% of 7227576 rows Read 16.9% of 7227576 rows Read 33.2% of 7227576 rows Read 49.9% of 7227576 rows Read 67.0% of 7227576 rows Read 83.4% of 7227576 rows Read 7227576 rows and 4 (of 4) columns from 0.214 GB file in 00:00:09 minFragLen = 150 maxFragLen = 40000 Filtered out 1110 interactions involving other ends < minFragLen or > maxFragLen. minNPerBait = 250 Filtered out 5210 baits with < minNPerBait reads.
Error in readSample(inputFiles, cd) : All interactions have been filtered out. Execution halted
Any assistance is much appreciated! Thanks Lea