Question about LiftOver - Forward and Reverse Strand?

[Priyanshi Shah]

Hello,

I hope you're doing well :)
I want to use LiftOver to convert specific genome coordinates from the hg19 genome assembly to hg38. I was wondering if there is a way to mention forward and reverse strands while mentioning the coordinates.

I'm attaching a picture of some of the coordinates I want to convert:

Thank you for your help!!

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Priyanshi

[Luis Nassar]

Hello,

Thank you for your interest in our tool.

If you would like to retain the forward/reverse information after you convert the coordinates, you can reformat your file into a BED 6 file (https://genome.ucsc.edu/FAQ/FAQformat.html#format1). For example,

chr5p: chr5:10001-13806 

would become:

chr5 1000 13806 chr5p 0 +

One of our engineers provided a short perl script that could perform the short conversion from a file like the one you have in your screenshot:

perl -wne 'chomp;
          ($name, $chr, $start, $end) = split(/[\s:-]/);
          print join("\t", $chr, ($start-1), $end, $name, "0", "+") . "\n";' \
    items.txt > items.bed

The outcome after you use liftOver (https://genome.ucsc.edu/cgi-bin/hgLiftOver) on these files will include the original strand of the item.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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