[Denovoassembler-devel] Planaria transcriptome coverage distribution

[David E. (gringer) <dav...@mp...>]

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