A quick question.
I am running bam2fastq and it ask to provide # for pair-end data. When I run the command in a bash script on server (as a part of a pipeline), it exits with errors beacuse the bash script understand # as a comment. Any solution for this??
-o FILENAME, --output FILENAME
Specifies the name of the FASTQ file(s) that will be generated. May contain the special characters
% (replaced with the lane number) and
# (replaced with
_2 to distinguish PE reads, removed for SE reads). [Default: s_%#_sequence.txt]