WT/Total counts in output .cdn matrix

[ggstatgen]

Hi Ted

Thanks for releasing ORFcall! I have just installed it and I am running it on some test data. I was hoping to ask you a few questions about its correct usage if that's ok.

So the basic output is a set of three files, the .cdn, the .aa, and the .indels report. My question is about the content of the .cdn file. It appears to report raw counts (please correct me if wrong) for every possible codon, with each row being one position in the ORF. Row 2 (soonafter the header) is, in my design, the Methionine (ATG). The last row reports count for the last aa before the stop codon (which I excluded from the fasta input contig with a ']' square bracket).

Hope this is correct so far. On to my question.

As I have not designed any mutations for the start codon, my 'codon_used.dat' file contains , for its row, only 0s, except for the 'ATG' column, where it has a '2' (WT).

Based on the above, I was expecting to find, in the .cdn output file, a count of 0s everywhere for the first row, except for the ATG column, where I expected to see an extremely high count (approximating the total number of reads in my fastq, minus errors in alignment). However, this position has a 0 too.

Having checked other amplicon positions in the .cdn output, it appears that all WT codons for every row have a count of zero.

Are you excluding the WT counts from the .cdn by design or is there something wrong in my input files?

NOTE - It would seem (again please correct me if wrong) that the totals are in the .indel file. Any chance to have ORFCall automatically plug those in the right column for each row in .cdn?

Thanks for your help!