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Why Shouldn'T I Use Masking When Doing A Reference Alignment?

Hi all,

What are the problems that are associated with hard or soft-masking my reference before doing a reference alignment using a tool like BWA or Bowtie?

repeats alignment reference
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updated by Biostar Biostar • written by Joseph Hughes Joseph Hughes

1 answer

Two related questions with answers:

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updated by Ram Ram • written by Istvan Albert Istvan Albert

Second link appears to be broken...

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written by swbarnes2 swbarnes2

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