deletions | additions       diff --git a/16S rDNA Sequencing and Analysis (Organism Identification).md b/16S rDNA Sequencing and Analysis (Organism Identification).md  index c7f07b0..4622b20 100644  --- a/16S rDNA Sequencing and Analysis (Organism Identification).md  +++ b/16S rDNA Sequencing and Analysis (Organism Identification).md 
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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) (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 
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###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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###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/ Desktop/Sanger_seq  Then, to run the script, type:  perl merge\_sanger\_16s.pl file1.fastq file2.fastq  The script will return one of 2 messages:  +"Found N conflicting case(s) during merging of X residues"   or  +"Not enough data to overlap confidently."   The newly merged file will be saved as file1_merged.fasta and can be uploaded to BLAST for identification.  The syntax to run the script is