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Old 10-27-2015, 10:59 AM   #50
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

That's an excellent question. I've never used Trinity. A post in their forum claimed that it will ignore the extra reads if you concatenate them to the end of one of the paired files. However, their faq claims the opposite:
If you have additional singletons, add them to the .fq file that they correspond to based on the sequencing method used (if they’re equivalent to the left.fq entries, add them there, etc).
So it sounds like probably you should, indeed, concatenate them at the end of the left reads. You can easily test this by using a single pair of reads (one read in the left and one in the right file), then concatenating all the unmerged reads onto the left file, then assembling. If if finishes almost immediately and nothing assembles, then it's ignoring the merged reads
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