Strand colour from BED file in IGV

Question

[victor_biotec]

Anyone know how I can change the feature colour of a track (BED file) based on strand orientation?

Example: chr 1 100 feature1 0 + chr 1 100 feature1 0 -

I want to colour the "+" feature RED and the "-" feature BLUE

Thanks a lot!

[Ram]

This is a question, not a forum discussion. I'll make the appropriate changes, but please be more careful in the future.

[victor_biotec]

Thank you! and sorry!

Answer 1

[Dan D]

Look here at the third example. You can set a line in the header of your BED file to automatically color by strand. IGV should pick that up IIRC.

[victor_biotec]

Thank you very much! The head of example 3 didn't function for me (I think that work only for Genome Browser), but with your information I could found that is possible to create a BED 9 file in where the last column have the colour in RGB. I only put as head the next: "track itemRgb=On"

     example
     track itemRgb=On
     chr    1000    2000    neg 0   -   1000    2000    "167,203,104"

So, I have the colour (of my option) for each strand (or each feature of BED file)

Grettings!

[Brunox13]

This was very helpful, thank you!

For anyone else who finds this - just delete the first line that says "example", and change the "chr" to an actual chromosome record name and this example will work.

Also, note that for this to work with your own data, you do need to have values in columns 7 & 8 (thickStart and thickEnd, respectively - see the BED format specification).