sebhtml/ray — Issue #41: Scaffolding should not use weak peaks in the distribution of outer distances
Author: sebhtml
Created: 2012-01-06 01:02:50+00:00
State: open

Submitted by : e-ozer@fsm.northwestern.edu

I'm doing assemblies of 100bp paired-end Illumina reads in Ray 1.7. I've been allowing Ray to automatically determine insert sizes, but I'm ending up with two peaks in the LibraryStatistics.txt files where I'm only expecting one. The insert sizes per my sequencing provider were ~ 235 bp, and Peak 0 shows an AverageOuterDistance of 205 and StandardDeviation of 45, but I'm also getting a Peak 1 with an AverageOuterDistance of 5205 and StandardDeviation of 30. Looking at the Library0.txt file, the vast majority of the insert sizes fall into the range of the lower peak, with about 215 reads falling into the upper range. Of the 13 different libraries I've assembled so far, 11 of them have this second peak. Unfortunately, these "long inserts" are being used by Ray's scaffolder to give me huge regions of N's in my scaffolds that I don't think are real. I checked with my sequencing provider and they thought it would be impossible for me to have mate pair contamination of my paired-end libraries since there's no circularization step, so I'm worried this might be a glitch in the automatic insert size determination of Ray. When I do a reference-based alignment with the same library, there seem to be no inserts larger than 517.