Adjust fragment size mean and standard deviation

[Nicklas Nordborg]

In the demux step we introduced a call to bowtie that is used to calculate the average fragment size and standard deviation (see [2680]). The values are used as input to Tophat for -mate-inner-dist and --mate-std-dev (see [2684]).

But after alignment Tophat reports values which are typically 13 (inner-dist) and 10 (std-dev) higher. Adjusting the input parameters with this amount gives higher alignment rate.

We tested effect of the ad hoc addition to the bowtie numbers on the overall tophat alignment, and compared the tophat aligned fragment lengths and widths with the input values to tophat. The net result is that the alignment rate increases approximately 3 per cent over a sample set of 150, and the lengths and widths are retained within a standard deviation of 0.02. (Data not shown.)

[Nicklas Nordborg]

(In [2788]) Fixes #658: Adjust fragment size mean and standard deviation

Added two configuration parameters that can be used to adjust the --mate-inner-dist and --mate-std-dev parameters to tophat. Default values are 13 and 10.