wildcard use for bowtie2 unpaired read sets?

[jgibbons1]

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

[kmcarr]

Stream the reads to stdout and then bowtie2 can read from stdin by specifying '-' for the -U option. For example:

gzip -dc *.fastq.gz | bowtie [options] -x <index> -U - -S output.sam

[jgibbons1]

Awesome...thank you @kmcarr...this worked perfectly

I also tried replacing "gzip -dc" with "zcat" and that seems to be a little faster

Thanks!