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Scripture Visualisation Tool Help Please

Hi,

When I try to view my .bed file with IGV it appears to be showing the entire chromosome rather than the region specified using -start and -end. If anyone knows what might be causing this and how to resolve a solution would be greatly appreciated.

Regards,

Kevin

visualization
• 2,640 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by User 7998 • User 7998

What do you mean by -start -end ? Can't you zoom in and out with the -and + buttons?

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written by Istvan Albert Istvan Albert

1 answer

Something like that ? The following script should tell IGV to go to the two genomic positions and to take some pictures that will be saved in /tmp/igv.

$cat script.sh

mkdir -p /tmp/igv
sleep 2
echo "snapshotDirectory /tmp/igv"
sleep 2
echo "goto chr3:100"
sleep 2
echo "snapshot"
sleep 2
echo "goto chr3:200-300"
sleep 2
echo "snapshot"
sleep 2

$ sh  script.sh |  telnet 127.0.0.1 60151
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

@Pierre : Is there a way to invoke "sleep" within IGV batch script...any comments?

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written by Rm Rm

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