Limit the number of reads loaded

[Mark Cowley]

Hi,
I’m loading high-depth BAM files via URL into IGV & often get a ‘500 Internal Server Error’ HttpResponseException. I assume this is a server-side issue, but wonder if I can mitigate this through optimising the IGV settings.

I also see IGV loading >10,000 reads despite setting the read down sampling to just 100 reads over 50bp windows. These reads are being loaded even after the initial reads coverage histogram have been rendered. Can you please advise of a setting to restrict the number of reads that IGV loads?

I’m using IGV version 2.3.90 on OSX.

Cheers,
Mark

[James Robinson]

Hi,

All the reads will be loaded, you can't control that,  the downsampling occurs afterward.   There is no way to "skip" reads,  until it's loaded you don't know its location or anything else about it.

A 500 error from a server is outside the control of the client.

Jim

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