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Old 12-22-2014, 06:03 AM   #1
morning latte
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Default Median basepair coverage of reads across contig length

Hello experts,

I am having hard time to understand a method from a metagenomic paper. The author used "median basepair coverage of reads across contig length" to measure base pair coverage of contigs. Does this mean that reads were aligned to contigs and length of contigs covered by reads were used? What does median mean here? Could anyone give me more detailed explanation on this? Any advice would be greatly appreciated.

Last edited by morning latte; 12-22-2014 at 06:07 AM.
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Old 12-22-2014, 08:45 AM   #2
westerman
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Perhaps if you give us a reference to the paper then we could figure out what the author meant.

As a wild guess since this is metagenomics thus implying multiple read sets aligned to each contig, I think that (1) the reads were aligned and (2) a coverage per contig per read set was obtained and then (3) a median per contig was found for all of the read sets. But as I say that an wild guess.
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