-
```
I have used Popoolation in the past and cited it in a publication, and I love
the software. I am sequencing viral genomes and am interested in very low
frequency viral variants in the population…
-
```
Hi,
I try to use Popoolation with .sam from Bowtie2 and not BWA, because Bowtie2
parameters interest me, but I obtain only "na" in the final output.
Despite many tests I don't find solution and…
-
```
This isn't really an 'issue', but it something for which the syntax is baffling
me. The read groups are assigned as such:
RG='@RG\tID:1\tPL:ILLUMINA\tSM:'$READ_GRP'\tDS:ref='$ASSEMBLY',pfx='$REF…
-
```
Hi,
A problem occured sometimes when converting mpileup to sync format of
popoolation:
perl mpileup2sync.pl --input Input.mpileup --output Output.sync --fastq-type
'sanger'
The error given is:
…
-
```
Hello, I'm just wondering if Mauve installation is required for other scipts
besides mauve-parser.pl ? I ask because I'd rather not install it if it isn't
necessary. Thanks.
```
Original issue …
-
```
What steps will reproduce the problem?
1. created mpileup successfully
2. created syn file successfully
3. fisher-test.pl fails (stops on line 9 and 10)
What is the expected output? What do you s…
-
```
What steps will reproduce the problem?
1. params used
perl Variance-sliding.pl --input example.pileup --output example.pi.txt
--snp-output example.snps.txt --measure pi --pool-size 25 --fastq-typ…
-
Hi,
I will love to use this tool for my analysis, till now I have been using Popoolation2. So I have sync files for my populations. I wanted to know the frequency table of alleles, is it a SYNC file …
-
Would it be possible to have the max read depth be a percentile? For example, set it to 0.98 to exclude reads with depth in the top 2% highest coverage. Perhaps, if the value passed to the parameter i…
-
Hi,
I went through all the past issue and hit the same problems as previous users.
/smsk_popoolation$ snakemake --conda-create-envs-only
Error: you need to specify the maximum number of CPU cor…