Recent changes to Tutorial

Discussion for Tutorial page

Mr Schweitzer — Tue, 07 Nov 2023 11:44:49 -0000

Hello Mr. Bennardo,
I think the two most common ways of adressing multiple testing in GWAS-like data is either using a Bonferroni corrected p-value threshold or by using a False Discovery Rate (FDR) approach. The documentation for the R package "qvalue" is very well written:
https://www.bioconductor.org/packages/release/bioc/manuals/qvalue/man/qvalue.pdf

Discussion for Tutorial page

Lautaro Ezequiel Bennardo — Tue, 07 Nov 2023 01:39:09 -0000

Hello everyone,
I am using popoolation2 to perform the CMH test between 4 pairs of populations. The issue is that it's giving me very high p-values in general (very low actually), less than 10e-60. Does anyone know how I should choose the p-value cutoff? Or if there's any correction I should apply to these values? Thank you!

Discussion for Tutorial page

Anonymous — Wed, 13 Sep 2023 14:09:55 -0000

Hi everyone,

I noticed that when converting an mpileup file to a sync file, positions on a genome are shifted.
For example, position 10,923,271 in a reference genome used for mapping was shifted to 10,923,753 in a sync file.
Does anyone know how to resolve this error?

Discussion for Tutorial page

Hafiz Muhammad Anas — Sun, 07 May 2023 17:10:17 -0000

Hello Community
Is it possible to annotate snps from snpeff eff tool after getting variants? which file i need to annoate?

Discussion for Tutorial page

Atikah — Wed, 09 Jun 2021 09:05:40 -0000

I just found out that it was rc SNPs not pop SNPs type.

Discussion for Tutorial page

Atikah — Wed, 09 Jun 2021 03:09:20 -0000

Hi everyone,

I am using Popoolation2 sofware to calculate allele frequency and Fst now. But when I calculate allele difference of my populations, it generates several locus with 1 allele count (only one allele state). Commonly SNPs is a biallele or in some cases it can contain 3 alelles or 4 alleles. And in the minimum coverage, I set it 10 but in the rc file it generates the SNP with coverage less than 10. Do you think there is an error that happening when I use the Popoolation2?
I am really appreciate if you can help me figured out what is happening. Thank you.

Discussion for Tutorial page

Mr Schweitzer — Sun, 04 Apr 2021 15:26:15 -0000

Hello Mr. Kengne,
I had the same problem and I managed to get the perl script running by following this solution in the comments here:
https://code.google.com/archive/p/popoolation2/issues/19

I hope this helps!

Discussion for Tutorial page

Jonas A Kengne — Tue, 02 Mar 2021 16:54:18 -0000

Hi Erica, I downloaded the online tutorial on popoopulation2 and had some problems in its execution. Could you assist pls?

problem

created mpileup successfully
created syn file successfully
fisher-test.pl fails (stops on line 9 and 10)

Exact message from the terminal:

poolseq_test$: perl popoolation2_1201/fisher-test.pl --input p1_p2.sync --output p1_p2.fet --min-count 6 --min-coverage 50 --max-coverage 200 --suppress-noninformative

Can't locate Text/NSP/Measures/2D/Fisher/twotailed.pm in @INC (you may need to install the Text::NSP::Measures::2D::Fisher::twotailed module) (@INC contains: /home/Jako/Documents/poolseq_test/popoolation2_1201 /home/Jako/Documents/poolseq_test/popoolation2_1201/Modules /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /home/Jako/Documents/poolseq_test/popoolation2_1201/Modules/FET.pm line 10.

BEGIN failed--compilation aborted at /home/Jako/Documents/poolseq_test/popoolation2_1201/Modules/FET.pm line 10.

Compilation failed in require at popoolation2_1201/fisher-test.pl line 9.

BEGIN failed--compilation aborted at popoolation2_1201/fisher-test.pl line 9.

Looking forward to hearing from you or any other person willing to help.

many thanks in advance

Discussion for Tutorial page

Maria Cortazar Chinarro — Sun, 03 Jan 2021 00:05:17 -0000

Please, can you upload the igv png images to check whether my results looks ok?
I cannot acces to thouse pictures:

"Voila, the result should look something like this:

Note that the result shown above only contain the Fst for a single pairwise comparison (pop1 vs pop2). PoPoolation2 is per default calculating the Fst for all possible pairwise comparisons between populations (when several populations are present in the synchronized file), and these results may just as easily be converted into the .igv format. When loaded into IGV it may look like the following:"
Thank you very much,

Tutorial modified by Robert Kofler

Robert Kofler — Sat, 28 Mar 2020 10:05:53 -0000

--- v1
+++ v2
@@ -35,7 +35,7 @@

 # Data

-The sample data can be downloaded here: <http: files="" demo-data.zip="" popoolation2.googlecode.com="">
+The sample data can be downloaded here: https://sourceforge.net/projects/popoolation2/files/demo-data.zip

 Subsequently unzip the archive. 

</http:>