What steps will reproduce the problem?
I have two sets of reads generated by two different technologies from the genome of a particular specie. I also have the genome of a similar specie as the reference genome.
1. I used MosaikBuild to convert the formats.
2. I used MosaikAligner to align each set of reads to the reference genome
separately.
3. I used MosaikCoverage to see the coverage profiles.
What is the expected output? What do you see instead?
The problem is that there is a big drop between mean coverage of the first 8
chromosomes and other chromosomes. The mean coverage is higher than what it
should be for the first group and far lower than the expected value for the
second group.
When I changed the order of chromosomes in the reference genome, the problem
resolved.
What version of the product are you using? On what operating system?
Mosaik-1.0.1388 / GNU/Linux Debian
Please provide any additional information below.
I repeated the process from the beginning with different input parameters, but
I got the same result. Then, I aligned the second set of reads to the same
reference genome and again, I had a weird drop in the mean coverage after
chromosome 8.
To resolve the problem, I changed the order of chromosome in the reference
genome and repeated the process from the beginning, using the previous set of
input parameters. Surprisingly, this time Mosaik aligned the reads more
uniformly and the result was similar to what I expected for the both sets of
reads.
One of the input sets contains almost 30 million single-end 76bp reads.
Original issue reported on code.google.com by ham...@gmail.com on 30 Jul 2011 at 1:45
Original issue reported on code.google.com by
ham...@gmail.comon 30 Jul 2011 at 1:45