visualizing the file with BigWig format

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6.5 years ago

lkianmehr ▴ 100

Hello

I am trying to visualize my Bigwig file with UCSC or IGV, about UCSC I don't know any about constructing custom tracks and can't do it, and IGV can't show it. how do I Construct a custom track in UCSC? or about IGV?

thanks

RNA-Seq ucsc visualize BigWig • 7.3k views

ADD COMMENT • link 6.5 years ago by lkianmehr ▴ 100

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Have you loaded the correct genome in the IGV? This tutorial might help. https://www.france-bioinformatique.fr/sites/default/files/EBA/V3-2014/Elodie_Giraud_visualisation-IGV_TP_EBA-2014-10.pdf

ADD REPLY • link 6.5 years ago by Sej Modha 5.3k

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thanks for your reply. yes, I have. I think IGV cant open BigWig file, it works just with convert it's format to TDF.

ADD REPLY • link 6.5 years ago by lkianmehr ▴ 100

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I can confirm that IGV can open BigWig files, I have used it in past with BigWig files, are you sure that your files are in correct format?

ADD REPLY • link 6.5 years ago by Sej Modha 5.3k

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IGV definitely supports BW format. Please check if you have the current version of IGV, and point out how these BWs have been generated, and what the error message is.

ADD REPLY • link 6.5 years ago by ATpoint 85k

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FYI I was having trouble also until I made sure the extension was .bw from call to bedGraphToBigWig

ADD REPLY • link 3.9 years ago by bjwiley23 ▴ 40

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