how to visualize Multiz results from genome browser

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Liu, Fei

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Sep 4, 2014, 7:28:08 PM9/4/14
to gen...@soe.ucsc.edu
Hi,

I'm wondering that if you can suggest me a tool to visualize the Multiz alignments from genome browser. The alignment results are currently displayed as discontinuous blocks, and I don't know if there's an option for getting an continuous output instead of alignment blocks. 
Many thanks in advance!

Best,
Fei

Matthew Speir

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Sep 5, 2014, 2:10:37 PM9/5/14
to Liu, Fei, gen...@soe.ucsc.edu
Hello Fei,

Thank you for your question about visualizing Multiz alignments. We recommend using the UCSC Genome Browser to visualize your alignments. If you have your alignments in MAF format, and we host the assembly used for the alignment, you can upload these alignments as a custom track. For more information on the MAF format, refer to the following help page: http://genome.ucsc.edu/FAQ/FAQformat.html#format5. More information on uploading custom tracks can be found here: http://genome.ucsc.edu/goldenPath/help/customTrack.html.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group
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