Running an IGV batch script helps increase the number of reads per image, compared with File | Save image
, but it does not solve the issue by itself.
To run a script, first make a script file like so with 1 command per line:
snapshotDirectory ./
goto chr2:28582094-28582790
maxPanelHeight 10000
snapshot chr2_28582094_28582790.png
Run the script using Tools | Run batch script
menu. The importat trick is the maxPanelHeight 10000
which is what makes this include more reads than the default snapshot.
You can also convert this into a little shell script:
#!/bin/bash
mkdir -p /tmp/igv
sleep 2
echo "snapshotDirectory /tmp/igv"
sleep 2
goto chr2:28582094-28582790
sleep 2
echo "maxPanelHeight 10000"
echo "snapshot chr2_28582094_28582790.png"
Then, just open IGV, load the relevant BAM file and run the script like this to connect to IGV via telnet (credit to Pierre Lindenbaum):
sh foo.sh | telnet 127.0.0.1 60151
File | Save image
, but it does not solve the issue. To run a script, first make a script file like so with 1 command per line:snapshotDirectory ./ goto chr2:28582094-28582790 snapshot chr2_28582094_28582790.png goto chr4:8203487-8203815 snapshot chr4_8203487_8203815.png
Run the script usingTools | Run batch script
menu. $\endgroup$maxPanelHeight
to get more reads). $\endgroup$