Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. Summary: Review Request: R-Rsolid - Quantile normalization and base calling for second generation sequencing data https://bugzilla.redhat.com/show_bug.cgi?id=611873 Summary: Review Request: R-Rsolid - Quantile normalization and base calling for second generation sequencing data Product: Fedora Version: rawhide Platform: All OS/Version: Linux Status: NEW Severity: medium Priority: medium Component: Package Review AssignedTo: nobody@xxxxxxxxxxxxxxxxx ReportedBy: bloch@xxxxxxxxxxxx QAContact: extras-qa@xxxxxxxxxxxxxxxxx CC: notting@xxxxxxxxxx, fedora-package-review@xxxxxxxxxx Estimated Hours: 0.0 Classification: Fedora Spec URL: http://verdurin.fedorapeople.org/reviews/R-Rsolid/R-Rsolid.spec SRPM URL: http://verdurin.fedorapeople.org/reviews/R-Rsolid/R-Rsolid-0.9.2-1.fc12.src.rpm Description: Rsolid is an R package for normalizing fluorescent intensity data from ABI/SOLiD second generation sequencing platform. It has been observed that the color-calls provided by factory software contain technical artifacts, where the proportions of colors called are extremely variable across sequencing cycles. Under the random DNA fragmentation assumption, these proportions should be equal across sequencing cycles and proportional to the dinucleotide frequencies of the sample. Rsolid implements a version of the quantile normalization algorithm that transforms the intensity values before calling colors. Results show that after normalization, the total number of mappable reads increases by around 5%, and number of perfectly mapped reads increases by 10%. Moreover a 2-5% reduction in overall error rates is observed, with a 2-6% reduction in the rate of valid adjacent color mis-matches. The latter is important, since it leads to a decrease in false-positive SNP calls. The normalization algorithm is computationally efficient. In a test we are able to process 300 million reads in 2 hours using 10 computer cluster nodes. The engine functions of the package are written in C for better performance. -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug. _______________________________________________ package-review mailing list package-review@xxxxxxxxxxxxxxxxxxxxxxx https://admin.fedoraproject.org/mailman/listinfo/package-review