Hello Jose, To split the samples, use "NGS: QC and manipulation -> FASTX-Toolkit for FASTQ data --> Barcode Splitter". Then use the "NGS: Mapping tools" to map. Using Galaxy would allow you to build the analysis path for one of the split samples (vs a single FASTA-format target gene), save the method as a workflow, then re-use the workflow for the remaining samples. Apologies for the delay in a reply, Best, Jen Galaxy team On 3/10/11 2:43 AM, Jochen Seggewiß wrote:

Hi!

Following situation: 10 barcoded "samples". Each sample consists of a mix of the sequences 3 independent genes (á 2 alleles). I would like to map the SOLiD4 reads only to the sequences of those 3 genes, patient by patient.

First, the 10 barcoded samples have to be separated from each other. Then, the short reads have to be mapped to the sequences of the 3 genes, which are available in FASTA-format (single) or multi-FASTA-format (all sequences in one file).

Is this possible using the available GALAXY tools? How?

Thank you in advance.

Jose

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