Hi Alex,
I am trying to use a parametersFiles, however, STAR cannot parse parameters from this file. Even when I use the
ENCODE.txt parameters, I get the following error:
EXITING: FATAL INPUT ERROR: unrecognized parameter name "--outFilterType" in input "/path/to/file/ENCODE.txt"
SOLUTION: use correct parameter name (check the manual)
I am really not sure why STAR cannot parse and use this file. I tried multiple STAR versions, including 2.7.10a_alpha_220601.
Thanks,
Babak