Changes between Initial Version and Version 1 of Ticket #658


Ignore:
Timestamp:
Oct 10, 2014, 3:27:10 PM (8 years ago)
Author:
Jari Häkkinen
Comment:

Legend:

Unmodified
Added
Removed
Modified
  • Ticket #658 – Description

    initial v1  
    22
    33But 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.
     4
     5We 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.)