whitespace at end of input_fastqs.txt file needs to be trimmed or it will miscount empty lines and make extra, blank, samples.
line 112 in scripts/circles/circle_star.sh works, while line 113 produces the error: ( n.b. syntax-error pointer is pointing at the "dot" in "circle_star.sh")
quoting around multiple filtering thresholds in cutoff list (per documentation) crashes the second-pass star alignment with error: (where "3" is the second filtering cutoff in "1 3 5 10")
"EXITING because of INPUT ERROR: could not open genomeFastaFile: 3"
Line 201 in scripts/circles/circle_star.sh does not check for a number of subjects or number of counts. Having 0 or 1 will fail the differential expression code un-gracefully.