#15 missing data and alternative start/stop codons with Syn/nonsyn-at-position.pl

[Anonymous]

Originally created by: maryro... (code.google.com)@gmail.com

I am using popoolation on bacterial sequence data and have a few questions about the Syn-nonsyn-at-position.pl. There does not appear to be documentation for the scripts contained in the syn/nonsyn folder of the program in the manual.

From the data I have generated, I am guessing that Syn-nonsyn-at-position.pl script will only calculate statistics for a gene after the first start codon - this causes a problem if the beginning of a gene has been removed due to poor mapping, repetitive region, etc or if the gene uses an alternative start codon. 

For example, I have a gene for which I am able to calculate pi; however, when I try to calculate the syn-nonsyn pi for the data this gene is not output. This gene is encoded with an alternative start codon. The last 4 bp of the gene have also been removed due to poor mapping.

geneX 29      0.999   0.000287201
geneX ***no output***

Do you have any suggestions or workarounds? I would very much like to calculate piN/piS for each gene.

Thank you!

[Rahia Mashoodh]

did you ever find the solution to this problem?

I'm also using a non-dmel genome and i can only get piN/piS for ~200 genes. I'm guessing this has to do with the start/stop codons as well ...