Bam2Fastq paired-end output options

Question

[GR]

Hi Everyone,

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 because the bash script understand # as a comment. Any solution for this??

BAM2fastq options:

-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 _1 or _2 to distinguish PE reads, removed for SE reads). [Default: s_%#_sequence.txt]

Answer 1

[Pierre Lindenbaum]

Did you put some single quotes around the argument?

[GR]

Done. Thanks! Sorry about the silly question.