Strand designation issue

[Peiyuan Zhu]

Hi,

Do I need to flip the alleles that are inconsistent with the assembly genome's strand designation before doing liftOver or will liftOver take care of this?

My coordinates are hg18 but since the data was collected without strand convention. Illumina has a tutorial on how they should be flipped https://www.illumina.com/company/video-hub/L96_y1_w-_s.html. Are there any tools you recommend to correct this? 

Best regards,

Gary

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

For BED input, LiftOver will use and respect the strand if specified as the 4th column. However, if no strand column is supplied, or the strand is ".", then Liftover defaults to the positive strand.

If you are referring to the SNP name, such as "C>A", then LiftOver will not modify the names. LiftOver only uses the coordinates to find a proper alignment between genomes.

To better assist you, can you provide an example that you are using as input for LiftOver?

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

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