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LosicLab / starchip

Detection of Circular RNA and Fusions from RNA-Seq
http://starchimp.readthedocs.io/en/latest/
MIT License
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Multiple usability issues #27

Open aubreybailey opened 5 years ago

aubreybailey commented 5 years ago
  1. whitespace at end of input_fastqs.txt file needs to be trimmed or it will miscount empty lines and make extra, blank, samples.
  2. 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") 
    "awk: cmd. line:1: { if (5 >= var) print /opt/modules/starchip/1.3e/scripts/circles/circle_star.sh >> var2 }"
"awk: cmd. line:1:                                                                             ^ syntax error"
  3. 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"
  4. 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.
kippakers commented 5 years ago

Thanks for the bug reports. Can you tell me what system you're working on?

Thanks, Kipp

aubreybailey commented 5 years ago

ubuntu 18 LTS package is installed as an environment module to mirror campus cluster "module" architecture