problems applying the scripts we had for LIRs to other SLiMs

[elenapapaleo]

When I try to apply our procedure (which works for the LIR) on BH3s motifs it seems not to produce the desired output and should be tested and debugged on the same case(s):
one of them is available here

/data/user/shared_projects/mavisp/ARID1A/slims/bh3s/slimfast