analysis paired end using tmap

[jeongmeani]

Hi,
these days, i got paired end ampliseq data.
so i want to run bismark using tmap to align to reference.
but i guess the bismark script of tools/bismakr_tmap does not support paired end when using tmap.

So i wanna modify something in that bismark script.
would you recommend anything?
or is there some possibility to run tmap to align paired end?

Best Regards.
Jeongmin

[spabinger]

Hi,

if you do not mind running your PE data with Bowtie2 than I would suggest to use our newest release with many more features and visualizations:
https://tabsat.ait.ac.at

In case of questions regarding the latest version, please see the contacts on this page:
https://tabsat.ait.ac.at/collaborate/

Integrating tmap into Bismark was quite a hassle, but you could start by searching for tmap in the source code. It might be worth checking out the latest version of Bismark to see if it is now easier to integrate another mapper.

Best wishes,
Stephan