Question: Displaying bam or bigwig files in UCSD genome browser
gravatar for mescobar
14 months ago by
mescobar0 wrote:


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 • 518 views
ADD COMMENTlink modified 14 months ago by Mo Heydarian790 • written 14 months ago by mescobar0
gravatar for Mo Heydarian
14 months ago by
Mo Heydarian790
United States
Mo Heydarian790 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 COMMENTlink written 14 months ago by Mo Heydarian790

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 REPLYlink written 13 months ago by mescobar0
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