Question: rDNA sequence extraction from NGS short reads or contigs
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gravatar for aoaahmed
4.0 years ago by
aoaahmed • 0
Saudi Arabia
aoaahmed • 0 wrote:

How can I extract rDNA sequence from NGS short reads or assembled contigs?

galaxy • 1.0k views
ADD COMMENT • link • modified 4.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.0 years ago by aoaahmed • 0
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gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

You can map them to a reference genome that also has an annotation track of ribosomal regions mapped, then correlate the two using the genome mapping coordinates.

Start out with the tools in these groups to do the correlation and see if those produce the result you are looking for:
Operate on Genomic Intervals
BEDTools 

Take care, Jen, Galaxy team

ADD COMMENT • link written 4.0 years ago by Jennifer Hillman Jackson ♦ 25k
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