deletions | additions       diff --git a/Genome Assembly and Annotation.md b/Genome Assembly and Annotation.md  index fab045e..e44f925 100644  --- a/Genome Assembly and Annotation.md  +++ b/Genome Assembly and Annotation.md 
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Create a new folder which will contain the files generated by the pipeline.  ###Running A5  Once you have opened the terminal navigate to the folder you just created because A5 will output the files your location when you call the program. In this exampleI created  the newly created  folder is  on the desktop and namedit  a5_ouput so the syntax for navigating to the folder is cd Desktop/a5_output/  Once there the easiest way to run the program is to drag and drop the a5 pipeline into the terminal. Open the bin folder located in the downloaded folder. Drag the file labeled a5_pipeline.pl a5\_pipeline.pl  into the terminal __add arrow to picture___  then drag in the input file(s) (the paired end read files). Finally name the output files   the final syntax will read