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!
Original issue reported on code.google.com by maryro...@gmail.com on 11 Nov 2014 at 8:00
Original issue reported on code.google.com by
maryro...@gmail.comon 11 Nov 2014 at 8:00