Hi all (and specifically @salzberg),
I've been trying to figure out a way to map a batch of unpaired fastq.gz files in the bowtie2 command line without manually entering a comma separated list of all of the files under the -U option. In some cases I have several hundred read files. Using the wildcard character in the command line isn't compatible, but I was wondering if there is another way to accomplish this.
Thanks
I've been trying to figure out a way to map a batch of unpaired fastq.gz files in the bowtie2 command line without manually entering a comma separated list of all of the files under the -U option. In some cases I have several hundred read files. Using the wildcard character in the command line isn't compatible, but I was wondering if there is another way to accomplish this.
Thanks
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