highlight specific exon with different color

[ssssyq1123]

hi, I want to draw a gene track using bed12 using bed display stacked, however, it only allow to set UTR region color, can I highlight some exons in the track also? how could I modified my data in bed12.

[lldelisle]

Hi,
Indeed we only allow different colors for CDS (coding) and UTR (non-coding). If you want to highighlight some exons, you can modify your bed12 so that the exons you want to highlight are the CDS and all the rest are non coding.
In a bed12 the CDS id defined in columns 7 and 8 see UCSC FAQ.
So if you modify the columns 7 and 8 you can get the resired output:

• Set all columns 7 and 8 to the same value as column 2.
• Change columns 7 and 8 for the intervals with exons you want to highlight with the coordinates of the exon.
  For example:

cat original.bed12 | awk -v OFS="\t" '{if ($4=="the name of your gene"){$7=start of highlight exon;$8=end of highlight exon}else{$7=$2;$8=$2};print}' > modified.bed12