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Question: Displaying bam or bigwig files in UCSD genome browser
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gravatar for mescobar
20 months ago by
mescobar • 0
mescobar • 0 wrote:

Hello,

I am attempting to view my RNAseq mapping file output (SAM) on the UCSC genome browser. This is Arabidopsis RNAseq data mapped to TAIR10. When I convert the SAM file to a BAM file, I get links to diplay the data in IGV, IBV, or bam.iobio. When I convert the SAM file to a BigWig file, I get links to display the data in IGB. However, no options to display in UCSC for either format. Can you help?
rna-seq bam • 821 views
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modified 20 months ago by Mo Heydarian ♦ 830 • written 20 months ago by mescobar • 0
0
gravatar for Mo Heydarian
20 months ago by
Mo Heydarian ♦ 830
United States
Mo Heydarian ♦ 830 wrote:

Hello, Thanks for reporting this. This issue has been filed here.

In the meantime, please try converting your SAM/BAM data to bedgraph formatted file in order for links to appear for UCSC genome browser and IGV.

Alternatively, you can always load your data manually to UCSC genome browser (if the appropriate header line has been added) by providing the copied link from the download icon of a dataset to the import portal for loading custom genomes.

Thanks for using Galaxy!

Cheers, Mo Heydarian

ADD COMMENT • link written 20 months ago by Mo Heydarian ♦ 830

Hi Mo,

Thanks for the help. Unfortunately, IGV won't load when I click on the link- I get a "localhost refused to connect" error message. This occurs regardless of whether the IGV link comes from a BED file or a BAM file. The UCSC browser isn't a good option, because they only have an old version of the Arabidopsis genome. Any ideas? Thanks!

ADD REPLY • link written 20 months ago by mescobar • 0
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