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Mask genes in primary contigs? #15

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MBMumphrey opened this issue May 27, 2020 · 0 comments
Open

Mask genes in primary contigs? #15

MBMumphrey opened this issue May 27, 2020 · 0 comments
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@MBMumphrey
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Most genes have a single sequence in the primary contigs for Grch38. Should we mask these? This way reads will no longer be biased towards a primary alignment in the primary contigs, even when the Grch38 seq is worse, and will all align to the provided alt contigs.
@MBMumphrey MBMumphrey added the question Further information is requested label May 27, 2020
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