Tophat Mapping Issue With Different Versions

Question

[User 0731]

Hi , I tried to map illumina ~2 million reads to Oryza sativa indica reference genome with its reference gtf file using different versions of Tophat 1.1.4, 1.3.0, 1.3.1, 1.3.2, 1.3.3 and the current one 1.4.1 . I used the defalut options just to check if the mapping statistics really gets affected. As a result, I got the following stats: Tophat1.1.4 Tophat1.3.0 Tophat1.3.1 Tophat1.3.2 Tophat1.3.3 Tophat1.4.1 2000000 2000000 2000000 2000000 2000000 2000000 227554 230817 231935 4517 231935 137724 I wanted to know why the number of reads mapped is varying in each version even though using the same data. Secondly, why there is a drastic change in the mapping stats with version 1.3.2 and 1.4.1 as compared with other versions? Can please anybody throw some light on this matter

Answer 1

[Weronika]

Do you know if the default options are the same between versions? If they're not, try running the analysis with explicitly setting all the same options and seeing if you get more similar results that way. And of course look into which default values changed and see if that explains the differences in your results.

If that's not it, the best way to find out what causes the difference would probably be reading the release notes for each tophat version to see what changed.