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niuhuifei / popoolation2

Automatically exported from code.google.com/p/popoolation2
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Sync file full of zeros #13

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Hi 

What steps will reproduce the problem?

I am trying to generate the synchronized files with the two options which are 
described in the manual (java and perl), I am expecting two columns with the 
allele frequencies of the two populations that I am using, but instead of that 
I have two columns full of zeros.

What version of the product are you using? On what operating system?

I am using version v1.201

Please provide any additional information below.

I am working with fastq type illumina

Original issue reported on code.google.com by ojrodrig...@gmail.com on 13 Dec 2013 at 4:39

GoogleCodeExporter commented 9 years ago 
Hi ojrodriguez,
most commonly the wrong fastq type has been provided if you receive only zeros.
So I suggest to double-check the quality encoding.
cheers ro

Original comment by RoKof...@gmail.com on 27 Jan 2014 at 3:50

ydorant commented 7 years ago

I'm using Popoolation2 on my poolseq data (Ion-proton sequencer) and I had the same pb. Keep in mind that illumina's quality encoding is moving. They returned to an encoding close to Sanger (see https://fr.wikipedia.org/wiki/FASTQ) So for my data I've only 0 with illumina encoding (so, what encording version is used in your popoolation2 v VS your illumina data ?). When I tried to use Sanger quality encoding, it's work well.

Y.