UCSC Viewer : Change color of the reads for stranded RNASEQ as IGV "first-of-pair-strand
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4.9 years ago
ZheFrench ▴ 420

By default, UCSC show reads colored by read strand as show here. In IGV you can do the same (color by "read strand')' but also you can use "first-of-pair-strand" coloration mode useful for stranded rnaSeq to separe sens and anti-sens reads.

I'd like to do the same with UCSC, is it possible ? How do you modify the track to have this same type of coloration mode.

UCSC IGV visualisation • 1.5k views
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UPDATE: there is something to do with bamColorMode=Tag and bamColorTag=? , Don't remember what bamCOlorTag is..

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This is a tangent but this feature is available in JBrowse 1.11.6+ with the "Use reverse template" option on alignment tracks. The "Use reverse template" option is sort of confusingly named, but achieves that same idea as "first of pair" coloring https://camo.githubusercontent.com/d317d83f9bd77aefde605a81c37602ba4ef90d9d/687474703a2f2f6b6f6b652e617372632e6b616e617a6177612d752e61632e6a702f484f57544f2f6a62726f7773652d62616d2d70652d737472616e6465642d636f6c6f722e706e67

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