Question: Popoolation variance-sliding.pl output shows only zero value
0
gravatar for bruseq
17 months ago by
bruseq20
bruseq20 wrote:

Hello

I am using Popoolation tool to calculate Tajima's D, Pi, and Watterson's Theta of my pool population by using "Variance-sliding.pl" script from mpileup data file . But the output generated shows 0 value in 3rd and 4th column and in 5th show "na". Eg:

4 125000 0 0.000 na

4 127000 0 0.000 na

4 129000 0 0.000 na

4 131000 0 0.000 na

4 133000 0 0.000 na

I follow the whole steps as per given in manual. So please guide me how to solve this above error, it's urgent.

Thank you,

Divya

ADD COMMENTlink modified 5 weeks ago by alex.zaccaron0 • written 17 months ago by bruseq20

Please anyone guide me how to solve this error.

ADD REPLYlink written 17 months ago by bruseq20
2
gravatar for lay_0
16 months ago by
lay_050
lay_050 wrote:

Hello diva, I hope this helps, I found this comment in the popoolation wiki website

"Values of 0 and na in my case came from using a bam file generated from reads using phred33 scores when the default of the Variance-sliding.pl script is to use phred64 encoding. Specify "--fastq-type sanger" to use the phred33 scoring scheme."

ADD COMMENTlink written 16 months ago by lay_050
0
gravatar for antaky
10 months ago by
antaky0
antaky0 wrote:

I am getting a very similar error for the d output. It gives number of snps found but no tajima's d value... I tried using both "--fastq-type sanger" and "--fastq-type illumina". Please any help? line example: dDocent_Contig_13 500 0 0.000 na

ADD COMMENTlink modified 10 months ago • written 10 months ago by antaky0
0
gravatar for minaljamsandekar
7 weeks ago by
minaljamsandekar0 wrote:

Any update for the answer? And where to provide --fasta-type option? I neither found this in popoolation nor mpileup.

ADD COMMENTlink written 7 weeks ago by minaljamsandekar0
0
gravatar for alex.zaccaron
5 weeks ago by
alex.zaccaron0 wrote:

Looks like Popoolation finds no SNPs within the sliding windows. That would explain why it is not calculating the measures. You could really have no SNPs in those regions, or there are SNPs but Popoolation is not considering them due to failing the filtering steps e.g. minimum quality. Keep in mind that Popoolation assumes by default quality phred encoding offset 64 (Illumina). If you have quality phred encoding offset 33 (sanger), you will have to set the parameter --fastq-type=sanger. Also, make sure you have coverage above the threshold set with the parameter --min-coverage (default is 4).

ADD COMMENTlink modified 5 weeks ago by genomax59k • written 5 weeks ago by alex.zaccaron0
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