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Old 11-24-2016, 11:57 PM   #2
Location: NJ

Join Date: Oct 2012
Posts: 97

All you need is Forward_Paired and Reverse_Paired reads. Those reads can be merged together using FLASH, a custom script (there are few here or on Biostar), or you may use Cyverse's Discovery Environment to Interleave the files together into one file.

The unpaired reads can be left alone for now, but in the future you may go back to them to reduce the number of them and so forth by playing around with the trimmomatic settings.

I hope this helps and all the best with your project.

Also check here for more tools that could help you out: with your project.
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