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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