Question: Bam2Fastq paired-end output options
gravatar for RT
5.7 years ago by
European Union
RT350 wrote:

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

BAM2fastq options:


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]

bam2fastq • 2.8k views
ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by RT350

did you put some single quotes around the argument ?

ADD REPLYlink written 5.7 years ago by Pierre Lindenbaum131k

Done. Thanks! Sorry about the silly question.

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by RT350
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