Question: Mapping To Only 3 Genes / Targeted Resequencing / Solid4 / Short Reads
gravatar for Jochen Seggewiß
7.7 years ago by
Jochen Seggewiß30 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
galaxy • 884 views
ADD COMMENTlink modified 7.6 years ago by Jennifer Hillman Jackson25k • written 7.7 years ago by Jochen Seggewiß30
gravatar for Jennifer Hillman Jackson
7.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Jackson
ADD COMMENTlink written 7.6 years ago by Jennifer Hillman Jackson25k
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