[Denovoassembler-devel] RE : Planaria transcriptome coverage distribution

[Sébastien B. <seb...@ul...>]

Hi David,

Any ideas why there are no peak in your transcriptome k-mer coverage distribution ?

Thanks.

> ________________________________________
> De : David Eccles (gringer) [dav...@mp...]
> Date d'envoi : 27 juillet 2011 08:32
> À : den...@li...
> Objet : [Denovoassembler-devel] Planaria transcriptome coverage distribution
> 
> For testing, here's the coverage distribution that was created by
> combining all the Smed RNA reads I have:
> 
> http://user.interface.org.nz/~gringer/hacking/planaria_Ray_5_2011-07-26_RayOutput.CoverageDistribution.txt
> [~140kb]
> 
> I had a bit of trouble with firefox freezing when I tried pastebin,
> which is why it's not there.
> 
> For what it's worth, some of these RNA transcripts (the low-expression
> transcripts) only have about 50-80 hits for reads from a single
> platform. While I don't expect to be able to get the sequences from
> these transcripts -- for one I looked at, the longest stretch with
> coverage greater than 5 was about 70bp -- it would be nice to have some
> way to tune Ray to work with RNA data that has similar distributions of
> coverage.
> 
> The analysis is as follows:
> 
> k-mer length:   31
> Lowest coverage observed:       1
> MinimumCoverage:        215
> PeakCoverage:   216
> RepeatCoverage: 217
> Number of k-mers with at least MinimumCoverage: 1944260 k-mers
> Estimated genome length:        972130 nucleotides
> Percentage of vertices with coverage 1: 64.0808 %
> DistributionFile:
> results/Ray_5_2011-07-26/RayOutput.CoverageDistribution.txt
> 
> I'm not quite sure I agree with a Peak/Repeat difference of 1, but given
> that I'm not sure what the numbers are used for, I'll leave that
> strangeness for someone else to comment on.
> 
> Note that it has a the big decrease in k-mers found for the first bit of
> the distribution. I'm not sure if this is because of the nature of RNA
> data or something else.
> 
> -- David
> 
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                  Sébastien Boisvert
                  http://github.com/sebhtml/ray