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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