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Question: Colors in IGV
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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?

ADD COMMENTlink 5.8 years ago navanax • 20 • updated 5.8 years ago Jorge Amigo 11k
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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.

ADD COMMENTlink 5.8 years ago Jorge Amigo 11k
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The link to IGVs default-color documentation did not work for me but it looks like it was point to this page

ADD REPLYlink 3.3 years ago
sviatoslav.kendall
• 480
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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."

ADD COMMENTlink 5.8 years ago Nicolas Rosewick 7.7k

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