skip comment lines of STAR chimeric output file

YangLab / CIRCexplorer2

circular RNA analysis toolset

http://circexplorer2.readthedocs.org/

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skip comment lines of STAR chimeric output file #56

Closed gudeqing closed 2 years ago

gudeqing commented 3 years ago

Hi, to avoid potential exceptions, I think we should skip the lines starting with '#' in Chimeric.out.junction, such as the following lines:

# 2.7.8a   STAR --runThreadN 6 --genomeDir /cromwell-executions/rnaseq_pipeline/......(**This line will be printed when set "--chimOutJunctionFormat 1"**)
# Nreads 931    NreadsUnique 18 NreadsMulti 0

best wishes!

kepbod commented 2 years ago

Please set --chimOutJunctionFormat to 0 (the default value) to not output comments in Chimeric.out.junction. See STAR manual for details.