Dear Akihiro,
Thank you for using the UCSC Genome Browser and your inquiry.
The discrepancy you notice is due to how we store the alignment coordinates. If you are unfamiliar with our coordinate system, please refer to the following blog post, The UCSC Genome Browser Coordinate Counting Systems. The minus strand coordinates in axt files are stored differently than how they are displayed in the Genome Browser. Specifically,
According to the axt format page, http://genome.ucsc.edu/goldenPath/help/axt.html:
If the strand value is "-", the values of the aligning organism's start and end fields are relative to the reverse-complemented coordinates of its chromosome.
You can use the following formula to convert minus-strand position format axt coordinates to Genome Browser display coordinates:
For BED format coordinates, use the following formula:
In this case, the size of chr8 in hg19 is 146,364,022 bp, so for the following position, chr8 89824042 89824491
, the conversion is:
and results in the following position: chr8:56,539,530-56,539,980
.
These coordinates are fairly close to the position you shared: chr8:56,539,781-56,539,981
.
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 Genomics Institute
Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining
--
---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To post to this group, send email to gen...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAOzs1aWipYpkfcXa2pfX6sfcoxytAERMXqTHc3ses9-vS8AMJQ%40mail.gmail.com.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.