Entering edit mode
8.5 years ago
noemichael
•
0
Hey,
I just got started and I wanted to control IGV through a port. But I have only a biology background... not really a computer-scientific one. Could somebody explain me how to control IGV through a port step by step. I searched the web, but I did not find a good tutorial. My final goal is to automatic plot the regions of interest, like discribed here: Automated Plotting Of Seq. Reads In A Bam File
I have BAM files, but not all INDELS are picked up. I find sometimes over 300% of extra INDELS. I want to look for them manually... So I wanted to print out the region of interest and annotate the reads on paper. Or does someone have a better idea?
Thank you
I don't think visually genotyping things is a particularly good idea - that's why we have computer programs to do it for us. You should probably work out either a) why your genotyper is missing indels or b) whether your missing indels are real by assaying them via another method.
If you wanted to do this for a legitimate reason, the way to do it is to write an IGV batch script. If you don't know any scripting languages and don't want to, you could probably manage to cobble a workable IGV batch script together in excel or something, with basically:
goto:chr1:1-1000
snapshot
goto:chr2:1-1000
snapshot
and so on for each location of interest. Save to a text file and open in IGV with "Tools- Load Batch Script". By default, this will produce a png for each region of the currently open IGV session named with the chr location (Probably in your home directory if you don't set anything). If you want svg instead, give each snapshot command a filename with .svg at the end.
Whether or not you SHOULD be doing it this way is another question. Good Luck!