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.
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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version 2.3.6
The link to IGVs default-color documentation did not work for me but it looks like it was point to this page