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igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
MIT License
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question about colors of alignments #1510

Open mocherry opened 7 months ago

mocherry commented 7 months ago

Dear all,

I have a short question about what the colors in alignments mean. image

there are the grey read alignments and the greenish ones. What is the difference.

Help would be greatly appreciated.

Thanks and best, Matthias

jrobinso commented 7 months ago

Please see the user documentation. I don't know what options you have chosen so can't answer the question directly, but you should find the answer in one of the sections on alignments, start here: https://igv.org/doc/desktop/#UserGuide/tracks/alignments/viewing_alignments_basics/