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Question: genomic regions without reads
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gravatar for kniazeva
3 months ago by
kniazeva • 0
kniazeva • 0 wrote:

Looking at custom BAM file with UCSC browser, I noticed that some reference genomic regions are not covered with reads. Does it mean that the regions have repeats and and the reads could not be placed unambiguously? Or is there another reason?
alignment • 127 views
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modified 3 months ago by Jennifer Hillman Jackson ♦ 25k • written 3 months ago by kniazeva • 0
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gravatar for Jennifer Hillman Jackson
3 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If your reads are not located in a particular genomic location, then either the reads really do not map there or you could try tuning the alignment tool's parameters. What reads are reported as mapped can vary between aligners.

Galaxy tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 3 months ago by Jennifer Hillman Jackson ♦ 25k
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