deletions | additions       diff --git a/16S rDNA Sequencing and Analysis (Organism Identification).md b/16S rDNA Sequencing and Analysis (Organism Identification).md  index e9de446..d932b6e 100644  --- a/16S rDNA Sequencing and Analysis (Organism Identification).md  +++ b/16S rDNA Sequencing and Analysis (Organism Identification).md 
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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" "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 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/ 
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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 fastq format, move all of them to the Sanger_seq Sanger\_seq  folder in which you saved the merge_sanger_16s.pl merge\_sanger\_16s.pl  script. Use the terminal to navigate to within this folder. Then, type: cd Desktop/Sanger_seq