Nicki, You are right that Galaxy's Bowtie only allows one input fastq. You would have to combine your multiple input files into one before running it in Galaxy. You can do this with the Concatenate datasets tool (under Text Manipulation). Let us know if you have any further questions. Regards, Kelly On Mar 4, 2011, at 11:49 AM, Nicki Gray wrote:

Hi

When running bowtie on the command line I was able to use more than one fastq file as input simply by listing them separated by a comma eg:

bowtie -p 3 -q -m 2 --best --strata --sam --chunkmb 256 /databank/ indices/bowtie/hg18/hg18 input1.fastq,input2.fastq output.sam

How can I do this within galaxy? The "Map with Bowtie for Illumina" tool only allows for 1 input fastq file as far as I can see.

Thanks, Nicki --------------------- Nicki Gray MRC Molecular Haematology Unit 01865 222434

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