i tried running Bismark on usegalaxy.eu but it didn’t work (toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_bowtie2/0.22.1+galaxy4). it seems the all mapping worked fine but then the files couldn’t be merged (see snapshot) .i am trying to aligned 2 paired end samples to TAIR10.
any help or advice are welcome
thanks a lot
thanks for reporting the error. There is a problem with the tool, could you try it tomorrow again?
Update: the problem was solved in this PR: Bismark: Fix subprocess command by gallardoalba · Pull Request #1110 · bgruening/galaxytools · GitHub