Scripture Visualisation Tool Help Please

Question

[User 7998]

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

[Istvan Albert]

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

Answer 1

[Pierre Lindenbaum]

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

[Rm]

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