Question: genomic regions without reads
gravatar for kniazeva
3 months ago by
kniazeva0 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
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by kniazeva0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
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