Replace bowtie stage with custom aligner in Tophat

[PBM]

Hi

I was curious to know if anyone has tried replacing bowtie stage with another aligner in tophat to measure the performance and also the accuracy of the results.

Kindly let me know if there is a possibility.

Thanks.

[gringer]

Kindly let me know if there is a possibility.

Certainly, there's a possibility. The tophat "excecutable" is python code, which makes it easier for a naive coder to hack other pieces in. Bowtie is used fairly heavily in the code, so you would need to replace quite a few sections with the alternative aligner, and work out what particular features of the output are necessary for the subsequent steps. This is made slightly easier because tophat is designed to work with both bowtie and bowtie2.