Reannotate Microarray Data

Question: Reannotate Microarray Data

8.2 years ago by

Dear Galaxy team, I just discovered your tool and is fantastic!. I want to reannotate the porcine affymetrix microarray. So I wanted to perform the following steps: 1. Run blat/blast to the porcine genome SGSC sscrofa9.2/susScr2 with the sequences of all probes on the array (which i have in a csv file) 2. Get genes 3. Do the same with human genome I can load my file and the entire pig genome but i do not know how to perform the "alignment" Is it possible to perform blat/blast (or any other alignment tool similar) through Galaxy? Thanks very much in advance, <mailto:lnonell@imim.es>Lara Nonell Microarray Analysis Service Scientific and Technical Services IMIM-Hospital del Mar Barcelona Biomedical Research Park (office 166) Doctor Aiguader, 88 | 08003 Barcelona Tel.+34 933 160 577 | Fax +34 933 160 410 lnonell@imim.es<mailto:lnonell@imim.es> www.imim.es<http: www.imim.es=""/>

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modified 8.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 8.2 years ago by NONELL MAZELON, LARA • 10

8.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Lara, Did you want to map the probes or the consensus sequences against the native genomes? Other (cross-species) genomes? If you really want to map the probes, using a tool such as NGS: Mapping -> lastz would be one choice. However, grouping probe results may be tricky if your goal is to annotate the array with genes/transcripts. If you want to map the consensus sequences, using a tool such as BLAT is preferred. BLAT would be best run on the command line and the results uploaded into Galaxy for further analysis. See http://www.kentinformatics.com/products.html. UCSC will also provide help for the tool genome@soe.ucsc.edu. For analysis, the tools in Galaxy can perform many analysis tasks, but you would need to design the workflow. The basic path would be to upload the reference genome mapping results (if needed), pull the gene annotation from UCSC or your favorite source with "Get data", and perform an interval comparison based on overlap to the reference genome. Tuning the tool parameters to get the best gene/transcript annotation per probe/consensus would be part of the scientific analysis process and may take some experimentation. Hopefully this helps to get you started! Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org

ADD COMMENT • link written 8.2 years ago by Jennifer Hillman Jackson ♦ 25k

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