I'm trying to run hostpot, and am getting the following error when using the test data and files provided:
run_pass2_hotspot: processing /home/ubuntu/hotspot/data/test_DNase_seq.hg19-pass2 generating 50kb pad set... May use bedops --help for more help. Error: Error: stat() failed on: stdin
When I try to process my own data, hotspot just quits during the
run_10kb_counts script, (no error message).
I'm a beginner to linux/command line/next-gen analysis, so it's quite possible I've made some very basic/silly errors. I have very closely followed the directions provided in the readme file, and am (fairly) certain I have all the required dependencies and have made the proper changes to the runhotspot and runall.tokens.txt files.
Any help or guidance would be greatly appreciated.