[Genome] strand in liftover application

[Kayla Smith]

Hello Asaf,

The liftOver tool takes as input either a position (which doesn't have a 
strand component) or a BED which may have a strand value.  If you 
provide a BED6 or higher, you will see the strand being maintained. 
When using a BED 3, 4 or 5, the liftover assumes that the input is + and 
returns results corresponding, but without reporting the resulting strand.

Here is a chart describing how the sign on the strand behaves:

input  chain   result
  +      +       +
  -      +       -

  +      -       -
  -      -       +

I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group


asaf levy wrote:
> Hi,
> 
> Does the strand data have any meaning in the liftover tool?
> 
> Is there a possibility that some genomic positions changed had their strand
> changed between different genomic versions?
> 
>  
> 
> Regards,
> 
> Asaf
> 
> TAU
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome