IGV - is it possible to adjust bases horizontally for misalignment
I am working on a set of aligned reads and I believe 10% of them were misaligned; for example:
CCAGGGGATC
-2-CCAGGAGATTC ("-2-" means IGV believes that there are 2 deletions and moved that read to the right for 2 positions.)
I want to move the second reads to the left for 2 positions, so it can be looked like:
CCAGGGGATC
CCAGGAGATTC
Can I do that in IGV? I am using IGV to check for misalignment but I cannot drag those misaligned reads over horizontally.
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colindaven
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Xinxin •
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Xinxin •
1 answer
You can use a tool like abra2 on github to do realignment. Results may vary, and it is computationally expensive.
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colindaven
True, but the question actually wants a solution, so with both answers combined then that solution might be attainable.
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colindaven
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