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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org