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Old 09-19-2015, 12:58 PM   #5
mcarson
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Location: Canada

Join Date: Sep 2015
Posts: 5
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Thanks for the suggestions, and I'm pretty confident in the reverse read primer as I get tens of thousands of hits when I search the different variants in a text file. I'll look into BBMap, are there any "standards" you'd suggest for places to start with options for BBDuk.sh in terms of trim length or quality? After those steps will I more or less be at the normal Sample_Lane_R1_001.fastq outputs most places send?

The labels are more for the filenames as QIIME seems to have automatic outputs that only allow you to alter the directory name not the actual output filename. So all of mine are now just Reverse/Forward.fastq when I want them to all be unique in some way so I can loop them through PANDAseq using a InputFilename txt file reference. I can just refernce individual directories that hold the files but it's more my OCD.
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