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Old 11-05-2010, 12:20 PM   #1
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Location: Europe

Join Date: Nov 2010
Posts: 9
Default Completely new to NGS

Hi everyone
I am completely new to NGS. I have been given some Illumina read files to get to grips with their data analysis and have some questions. The reads are not whole genomes but different genes, extracted using pcr primers.

-Firstly, what exactly is meant by genome 'coverage' or when someone says coverage = 2x? Does that mean that the sequences have been split into 2 and sequenced? Im a little confused on the definition of coverage

-I am using velvet to assemble these gene reads. Is there any logic in setting velvets parameters to auto? or would using velvet optimiser be the best way to go?

-does keeping the coverge cutoff parameter low mean you are guaranteed more contigs such that a high value misses out on possible contigs.

Sorry about the noob questions
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Old 11-05-2010, 06:35 PM   #2
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Location: Boston area

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Coverage = (total number of bases generated) / (size of genome sequenced).

So 10X coverage of a genome means on average each base has 10 reads atop it; in reality the distribution will not be uniform.

(I'm not experienced with velvet; will let someone else tackle that)
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