negative strand to positive strand coordinate conversion

[Henagan, Tara M]

Hi,

I understand that in the custom genome browser, all data map to the positive strand and only coordinates for the positive strand are shown in the browser. Thus, any data for genes that are encoded on the negative strand, are shown on the positive, with positive coordinates (not the negative strand coordinates). However, when I download the RefSeq Genes table from the UCSC database or use the other available tools from the website to annotate my data, start and end positions for genes encoded on the negative strand are given as coordinates on the negative strand. Therefore, these coordinates do not match the coordinates when I browse for the gene in the browser. 

My particular gene of interest is PPARGC1a. With the mm9 genome, the browser gives a  start position of chr5:51845488 and end of 51945160. The Ref Seq table gives a start (transcription start) of 51454249 and end of 51553921. 

How do I convert the coordinates from the RefSeq Genes table to the coordinates in the browser? In other words, what is the formula to convert coordinates from the negative to the positive strand?

It seems that I should be able to do the chromosome size - negative strand start = positive strand end. However, this does not work.

Also, the website says there is a convert utility that will do batch coordinate conversions and supports conversions between forward and reverse, but when I go to the website look for the tool, it appears that I can only use this utility to convert across genomes. Is there an available tool/utility to batch convert coordinates on the negative/minus strand to coordinates on the positive/plus strand?

Thank you,

Tara

[Pauline Fujita]

Hello Tara,

The discrepancy you are seeing is between different mouse assemblies.
The coordinates for PPARGC1a are as follows:

on mm10/GRCm38:
chr5: 51,454,249-51,553,921

on mm9/NCBI37:
chr5:51,845,488-51,945,160

Regarding transforms of negative strand coordinates, you might find
this wiki by one of our developers useful:

http://genomewiki.ucsc.edu/index.php/Visualizing_Coordinates

For a more general background on the peculiarities of UCSC coordinates
please also see this wiki:

http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms

Note that here at UCSC everything is referenced related to positive
strand coordinates even for negative strand items.

Hopefully that was 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.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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