WARNING long repeat for junction

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Maria Arceo

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Mar 12, 2021, 4:01:27 PM3/12/21

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Hi
I get a warning when aligning most of my reads:
*** long repeat for junction # 112714 : chr15 88855522 88855578; left shift = 14; right shift = 255 ***
It seems to be a common warning in general, and I wonder what it means
Thanks

Alexander Dobin

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Mar 20, 2021, 5:38:50 PM3/20/21

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Hi Maria,

this means that there is micro-repeat around the junctions, which mean the donor and acceptor can be shifted by 14 and >=255 bases to the right and left respectively without changing the spliced sequence.

It's OK if it happens for a few junctions, ~100 or less.

Cheers

Alex

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