deletions | additions       diff --git a/16S rDNA Sequencing and Analysis (Organism Identification).md b/16S rDNA Sequencing and Analysis (Organism Identification).md  index 75fa392..2e33c6c 100644  --- a/16S rDNA Sequencing and Analysis (Organism Identification).md  +++ b/16S rDNA Sequencing and Analysis (Organism Identification).md 
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2. To add files go to Traces and click on Add trace files, then select the reads   (.abi files) you want to work with.   3. The program is able to recognize forward and reverse reads from information in the file name if they are properly formatted.  + 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.  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.