Thank you! This solution works well and is very helpful.
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taraeicher •
Color Bed Track Annotations by Name
I am trying to upload a custom BED track to the UCSC Genome Browser. This track contains annotations from ChromHMM's 15-state model, i.e.
chr10 0 119600 15_Quies
chr10 119600 120400 1_TssA
chr10 120400 136200 14_ReprPCWk
chr10 136200 139400 15_Quies
chr10 139400 145200 9_Het
chr10 145200 162800 15_Quies
chr10 162800 165000 9_Het
chr10 165000 176200 15_Quies
chr10 176200 176600 7_Enh
chr10 176600 177000 5_TxWk
What I want to do is to visualize this track with a different color for each annotation. However, the closest track parameter I can find is itemRgb = On, and to use that I would need to manually add a separate color for each annotation in the BED file. Is there an easier way for me to do this, or if not, is there a one-line command I can use to add in the RGB values?
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Pierre Lindenbaum
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taraeicher •
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taraeicher •
1 answer
using awk to insert tge missing BED columns until the RGB column:
awk '{c="255,0,0";if($4=="15_Quies") {c="0,255,0";} else if($4=="1_TssA") {c="0,0,255";} printf("%s\t0\t.\t%s\t%s\t%s\n",$0,$2,$3,c);}' your.bed
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Pierre Lindenbaum
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