Question on batch lift-over between genome assemblies
K. van Duijvenboden
I have a question about lift-overs between genomes (inter-species). I know the batch lift-over tool can be used to convert a list of genome coordinates into a list of corresponding genome coordinates on a genome of choice (above a certain threshold of choice). However, this only results in the coordinates, not the % identity of the found matches.
I also know you can find the % identity for individual queries by going to View > In other genomes (convert) when browsing a genome. But this option does not appear to be available in batch.
Is it possible to batch convert genome coordinates whilst reporting % identity?
I hope my question is clear. Thanks for your help in advance.
Best regards,
Karel van Duijvenboden
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Jonathan Casper
Hello Karel,
Thank you for your question about liftOver results. Unfortunately, there is currently no way to make the website or command-line liftOver tools report the same information about result quality that the genome conversion tool provides. There is a way, however, to set up thresholds for those scores. The liftOver tools will then only report results with scores at least as high as those thresholds.
There are two parts to the quality score - the span, which is the percentage of the region in the first genome that was mapped to the second by the chain, and the percentage of bases in the first genome that were aligned in gapless blocks to the second genome. The difference between the two is that the span score includes bases that are part of a "chain" (a linked series of gapless blocks aligned between the genomes), while the base percentage score only includes those bases that were actually in the gapless blocks. More information about chains and nets is available at the following wiki page: http://genomewiki.ucsc.edu/index.php/Chains_Nets.
You can set up a threshold similar to the span score by using the "Minimum chain size in target" option for the liftOver tool. Instead of a percentage, the threshold value will be a minimum number of bases that must be mapped from the region in the first genome to the second. A liftOver with a minimum chain size in target of 1000, for example, will only report results where the chain contained at least 1000 bases of the region in the first genome.
The "Minimum ratio of bases that must remap" value in the liftOver tool is the minimum number of bases that must be directly aligned in gapless blocks from the first genome to the second. The value is usually set to 0.95 for lifts between assemblies of the same species, as they are expected to be very similar. For inter-species lifts, you may need to reduce that value to find any results; we typically use 0.1. I should note that the use of this value is a bit different from the "percentage bases" score in the convert tool. For the convert tool, the value is the percentage of bases in the entire region of the first genome that were found in gapless blocks aligned to the second genome. For the liftOver tool, the value is instead the percentage of bases mapped to the second genome that were found in gapless aligned blocks. This difference is a bit subtle, but means that the conversion tool will assign low scores to chains that match only a small piece of your region of interest, while the liftOver tool might still assign a high score (if the part of the chain that matches is mostly gapless aligned blocks).
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Jonathan Casper
UCSC Genome Bioinformatics Group
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