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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
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minigraph -S call missing data #58

Closed Xavster838 closed 2 years ago

Xavster838 commented 2 years ago

Hello, I'm trying to get minigraph segment coordinates in both query space and reference space. So far I have relied on minigraph's -S flag to output this to a GAF with () lines. I'm finding that for some segments these coordinates are failing to be outputted to the () lines. I am only getting the < ‘*’ segName segLen nMinimizer seqDiv segStart > columns, and failing to get the columns. Is there an alternative you would recommend to getting these datapoints?

Thanks

Xavster838 commented 2 years ago

I looked into the GAF a bit more. I'm seeing that the rows lacking the data i was looking for have zero minimizers in the mapping, and the flanking mapping segments are usually very close to each other within the query space (usually under 1kb, no greater than 5kb). I think there may be a missing link in the graph between the two flanking segments.

lh3 commented 2 years ago

You are correct that minigraph doesn't report coordinates for segments without hitting minimizers.

With the release of 0.17+, it is now recommended to generate graph and does alignment with option -c which enables base alignment. You should be able to get more detailed information by parsing the cg:Z tag in the GAF output.