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I am trying to use Illumina mate pair data to link scaffolds together in order to improve the assembly of a specific region of a eukaryotic genome. I used Bowtie to find mate pairs whose ends map to different scaffolds within the region and am now trying to use this data to piece the scaffolds together. However, I am finding some strange things when I look at the orientation information provided by Bowtie (column 2 of the output file). The orientation given by Bowtie is often different to what I get if I just blast the mate pair sequence against the scaffold it has been matched to.
To try to make some sense of this, I blasted all the mate pair sequences against the scaffolds and there the results were even more strange; 3563 of the 3566 sequences were plus/plus matches (i.e. had the same orientation as the scaffold). This seems very unlikely and I am not sure what to make of all this. Does anyone have any ideas?
To try to make some sense of this, I blasted all the mate pair sequences against the scaffolds and there the results were even more strange; 3563 of the 3566 sequences were plus/plus matches (i.e. had the same orientation as the scaffold). This seems very unlikely and I am not sure what to make of all this. Does anyone have any ideas?