Hello,
> ________________________________________
> De : Aarti Desai [aarti_de...@persistent.co.in]
> Date d'envoi : 12 septembre 2011 08:55
> À : Sébastien Boisvert
> Objet : Question on RAY
>
> Hi Sebastein,
> My name is Aarti Desai and I am using Ray to do assembly of some e coli and
> yeast illumina data. The problem is I have high level of duplication in the
> dataset. It is 87% in the e coli data (avg depth is about 800) and abt 56% in
> the yeast data (avg depth about 275X) as estimated using FASTQC. From what I
> understand, FASTQC uses the first 50bp of a read to identify duplicates in
> the dataset.
>
> I want to know how Ray handles duplicate reads in a dataset? Does it ignore
> duplicate reads?
Ray will count the k-mers in all the reads, build a distributed graph and find
paths in it.
The maximum k-mer coverage in Ray is 65535, so technically that won't be a
problem.
You just have to be sure that the reads are mostly randomly distributed across
the genome.
You can do some quality control with Ray too. Just run it on your data with:
mpiexec -n 24 Ray -k 31 -p 1_1.fastq 1_2.fastq -p 2_1.fastq 2_2.fastq -o
QualityControl
Then, you check this file:
QualityControl/CoverageDistributionAnalysis.txt
k-mer length: 31
Lowest coverage observed: 2
MinimumCoverage: 33
PeakCoverage: 108
RepeatCoverage: 183
Number of k-mers with at least MinimumCoverage: 9097604 k-mers
Estimated genome length: 4548802 nucleotides
Percentage of vertices with coverage 2: 33.1731 %
DistributionFile: coli/CoverageDistribution.txt
If the estimated genome length is correct, then these duplications should not
be a problem.
This estimation is done on the distributed graph before attempting to assemble
anything.
If most of the genome positions have simply no reads because most of the reads
come from a few highly represented regions, then this will be a problem with
any assembler.
What is exactly the 87% ?
Sébastien
http://github.com/sebhtml/ray
> Thanks for your help.
> Aarti
>
>
> Dr. Aarti Desai | Domain Specialist – Life Sciences Domain
> aarti_de...@persistent.co.in<mailto:aarti_de...@persistent.co.in> | Cell:
> +91-9673009492 | Tel: +91-20-30236348
> Persistent Systems Ltd. | Partners in Innovation |
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