Negative Strand Entry Representation Bed file

[mayur.d...@gmail.com]

I want  make bed file manually with entries corresponding negative strand.
As bed tool discards the entries where start coordinate  is lesser than end coordinate,I need help to include negative strand entries.

if any one explains it with example it will be good.

[Aaron Quinlan]

Hi Mayur,

BED format keeps coordinates the same whether an interval is on the forward or reverse strand. All one needs to do is use a "+" or "-" in the strand column (#6). When "+", it is implied that the start column (#2) is the start of the feature. However when "-", it is implied that the start of the feature is actually the end column (#3).

- Aaron

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[ree...@gmail.com]

I've recently tried putting a - my strand column ($6) but closestBed returns: "Error: malformed BED entry at line 3. Start was greater than end. Exiting."

To get around this I wrote an awk script to manually swap the start and end if the end is greater than the start but I'd like to know what I'm doing wrong.

Thanks!

-Reed

[Aaron Quinlan]

It sounds as though you are representing your reverse strand features by swapping the start and end coordinates. Bed format always keeps the start as the lower coordinate and end as the higher. Is that the case? If so, you will need to keep the start <= end.

- Aaron