I'm using IGV to visualize read coverage for a de novo trancriptome. Some of my mapped reads show up as different colors, green or red. I can't find any reference to these colors in the manual. How is a read that is highlighted in red/green different than one that is just grey?
the default IGV colors are well documented here, but if you right-clic on the reads you will find a "color alignments by" section, which will allow you to use colours to distinguish different read properties such as strand, sample, read pair and so on.
The link to IGVs default-color documentation did not work for me but it looks like it was point to this page
That link is also dead now, so I pulled this from an archive. Assuming this is paired-end data and you're coloring by insert size and/or pair assignment:
Blue is for inserts that are smaller than expected
Red is for inserts that are larger than expected.
Shades of green, teal, and dark blue show structural events of inversions, duplications, and translocations.
Color assignments depend on sequencing platform.
Other Color by options are described in the alignment track pop-up menu options
Could you put a screenshot of your alignment please. But it seems to be paired reads where each pair is on different chromosomes :
" IGV colors paired-end alignments whose inferred insert size is larger than expected or whose mate read is aligned to a different chromosome. A read with a mate aligned to a different chromosome is color-coded to identify the other chromosome."
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