deletions | additions       diff --git a/16S rDNA Sequencing and Analysis (Organism Identification).md b/16S rDNA Sequencing and Analysis (Organism Identification).md  index c2592dc..9e1efb3 100644  --- a/16S rDNA Sequencing and Analysis (Organism Identification).md  +++ b/16S rDNA Sequencing and Analysis (Organism Identification).md 
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+ Go to Traces and click on Find and mark forward/reverse. The default setting looks for _F for forward and _R for reverse. This can be edited in the Project settings (you can pull it up by clicking on the picture of the tools at the top of the page) and changing the search strings under trace settings  + If the program is able to recognize the forward/reverse reads it will place an orange left pointing arrow in front of reverse reads and a blue right pointing arrow in front of forward reads. This step is not necessary to get a consensus sequence, it just makes organizing the reads easier.   4. Pull up the Project Settings by clicking on the picture of tools at the top of the page. Click on the Sequence Processing tab, under Sequence trimming unclick the Automatically trim sequence ends button. You should also decrease the Min. confidence score under Consensus settings. The default option is 30 which represents a 99.9% quality score, for many reads this will be too stringent and will not allow you to get enough overlap to create a quality consensus sequence. A minimum confidence score between 15 and 25 is normally okay but tuning may be required depending on your read quality.  5. Group your forward and reverse reads by highlighting both of them and clicking Group selected forward/reverse files (under Traces)  6. Under Sequences go to Generate Finished Sequences and click on for all trace files. (you will need to redo this every time you change the project settings).  7. To view your consensus sequence, click on the read pair group and then click on the magnifying glass at the top of the page. You should see something like this