Cytoband map is very low-res in IGV

Karmella Haynes

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Mar 27, 2020, 4:39:33 PM3/27/20

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Hello. I would like to determine which specific cytoband a gene is located in. I would like to use the IGV browser instead of the one at UCSC, because IGV loads more quickly. However, the cytoband map at the top of the IGV window does not label all cytobands. Can the specific cytobands be displayed as a track based on the table from the UCSC Genome Browser database?

James Robinson

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Mar 27, 2020, 4:54:06 PM3/27/20

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Hi, that could be done, not possible now. I created a git issue, but no ETA on this https://github.com/igvteam/igv/issues/786

Is this possible at UCSC?

On Fri, Mar 27, 2020 at 1:39 PM Karmella Haynes <khayn...@gmail.com> wrote:

Hello. I would like to determine which specific cytoband a gene is located in. I would like to use the IGV browser instead of the one at UCSC, because IGV loads more quickly. However, the cytoband map at the top of the IGV window does not label all cytobands. Can the specific cytobands be displayed as a track based on the table from the UCSC Genome Browser database?

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Karmella Haynes

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Mar 27, 2020, 5:38:43 PM3/27/20

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Thank you for your reply. Yes, this track can be displayed at UCSC. Please see the screen shot above (drak grey and light grey bars). To view this track I set "Mapping and Sequencing > Chromosome Band" to "full."

On Friday, March 27, 2020 at 4:54:06 PM UTC-4, James Robinson wrote:

Hi, that could be done, not possible now. I created a git issue, but no ETA on this https://github.com/igvteam/igv/issues/786

Is this possible at UCSC?

On Fri, Mar 27, 2020 at 1:39 PM Karmella Haynes <khayn...@gmail.com> wrote:

Hello. I would like to determine which specific cytoband a gene is located in. I would like to use the IGV browser instead of the one at UCSC, because IGV loads more quickly. However, the cytoband map at the top of the IGV window does not label all cytobands. Can the specific cytobands be displayed as a track based on the table from the UCSC Genome Browser database?

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