deletions | additions       diff --git a/16S rDNA Sequencing and Analysis (Organism Identification).md b/16S rDNA Sequencing and Analysis (Organism Identification).md  index b4c853e..be27167 100644  --- a/16S rDNA Sequencing and Analysis (Organism Identification).md  +++ b/16S rDNA Sequencing and Analysis (Organism Identification).md 
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SeqTrace provides excellent directions for using the program at https://code.google.com/p/seqtrace/wiki/WorkingWithProjects  ##Edit and Create a Consensus Sequence with SeqTrace  For this workflow we have found that the following is the simplest way to edit and create a consensus sequence from a forward and reverse read in SeqTrace.  1. Create a new project (File > New Project)  
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8. The Trace View shows the quality scores, the chromatogram display, and the raw base calls from both the forward and reverse reads, as well as the consensus sequence. The consensus sequence is the middle list of nucleotides. If the program is giving you a string of Ns where your forward and reverse reads do not overlap, you need to decrease the Min confidence score.  9. To export the consensus from the trace view, go to File and click on Export working sequence. This will create a file containing the consensus sequence, which you can upload to BLAST and use to identify the organism.  ##Custom Script to Create a Consensus Sequence (merge_sanger_16s.pl)  ###Download/Install  1. Create a new folder called Sanger_seq somewhere on your computer  2. Download the script from https://github.com/gjospin/scripts  3. Download a zip of all of the files, unzip it and move the merge_sanger_16s.pl script to the Sanger_seq folder  ###MUSCLE  In order to run this script you will need to download MUSCLE (REF) from here: http://www.drive5.com/muscle/downloads.htm. Use the Archive Utility to open the file, change the name of the executable file from something like "muscle3.8.31_i86darwin64" to "muscle," and move it into your Applications folder.  ###Convert Files from .abi to . fastq  To run the merge_sanger_16s.pl you will first need to convert your read files from .abi to .fastq  This can be done at   http://sequenceconversion.bugaco.com/converter/biology/sequences/  Use the drop down menus to set it to convert .abi files to .fastq. Upload a file and convert it. The converted file will save to your downloads folder under the name sample.fastq. If you are working with a lot of reads we recommend immediately renaming the files to match the original abi file name to avoid confusion.  ###Edit and Create a Consensus Sequence  Once all of your files are in the fastq format, move all of them to the Sanger_seq folder in which you saved the merge_sanger_16s.pl script. Use the terminal to navigate to within this folder. Then, type:    cd Desktop/Sanger_seq/  The syntax to run the script is