stevekm/IGV-snapshot-automator

Only output IGV_snapshots.bat without *png

Closed this issue · 2 comments

zhangzhiyangcs commented

Hi,
I meet the error when I run IGV-snapshot with comand: python IGV-snapshot-automator-master/make_IGV_snapshots.py -r test.bed -o igv -g ./genome.fa -mem 64000 -s test.bam. There were no error. My bam file size is 80GB.
But when I just extract bam files with positon in test.bed. It works and output *png. Why cause this? Thanke you.

stevekm commented

Hi, I am not clear what exactly the problem is? You are not getting any PNG outputs in the first case which you described? Note that your .bed file must contain coordinates for the script to work; if you inspect the .bat file you will see that its simple instructing IGV to take snapshots at the regions in the .bed file. So if the .bed file is empty, there will be no instructions in .bat to take snapshots. Let me know if this helps.

stevekm commented

closing this one, let me know if you need any more help, thanks