deletions | additions       diff --git a/Data Submission.md b/Data Submission.md  index c94dd03..df86489 100644  --- a/Data Submission.md  +++ b/Data Submission.md 
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Run the fasta2agp.pl script included with A5 on the scaffold file outputted from the A5 assembly "my_scaffolds.fasta".   Syntax is:   $  perl fasta2agp.pl my_scaffolds.fasta > my_scaffolds.agp eg   $  perl /Users/Madison/Desktop/a5_miseq_macOS_20140113/bin/fasta2agp.pl /Users/Madison/Desktop/a5_miseq_macOS_20140113/example/phiX.a5.final.scaffolds.fasta > phiX.a5.scaffolds.agp If this runs successfully then you should see a both the .fsa and .agp files in your current directory. 
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Important Note: NCBI considers a gap of less than 10 nucleotides to be "missing information" in a contig, not a gap between contigs (whereas A5 has no minimum gap size). Therefore NCBI requires that contigs separated by less than 10 nucleotides be merged. This script performs that merging, meaning that the number of contigs in the .fsa file may be less than in your input file. Therefore we recommend counting the contigs in the .fsa file:  To count them in the terminal use the syntax  $  grep -c “>” name_of_your_.fsa_file Important Note: If after running the fasta2agp.pl script and counting the contigs you have the same number of contigs as starting scaffolds, then you should only submit the .sqn file to Genbank and say that scaffolding did not take place (otherwise NCBI will reject the .agp file).  
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Syntax is:  $  chmod 755 tbl2asn Once you have changed the permissions, create a new directory and place tbl2asn along with the .sbt file and .fsa files into the folder.  Run the tbl2asn program using the following syntax. You will need to fill out the organism name, strain, location, collection date, isolation source specific to your own project.   $  path_to_program/tbl2asn -p path_to_files -t template_file_name -M n -Z discrep -j "[organism=X] [strain=X] [country=X: city, state abbreviation] [collection_date=X] [isolation-source=X] [gcode=11]" Following the -p is the path to the directory containing the .fsa file, following the -t is the path to and name of the template file  Sample syntax  $  Desktop/ncbi/tbl2asn -p ~/Desktop/ncbi -t ~/Desktop/ncbi/template-1.sbt -M n -Z discrep –j "[organism=Ruthia magnifica str. UCD-CM][strain=UCD-CM] [country=USA: Davis, CA][collection_date=2002][isolation-source=Calyptogena magnifica tissue][gcode=11]"  
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Note that the only acceptable file types for fastq files are gzip (.gz) and bzip (.bz2). To gzip files in the Terminal use the following syntax:  $  gzip [filename] After completion, return to EMBL (the new submission tab of the SRA Webin submission system) and select the Next button. During this process, refreshing the page or navigating away from the page will reset the form and the information will be lost.