-
Hi
I am working on developing SNPs for radseq data and trying to use DiscoSnpRad to find SNPs and used the following code;
run_discoSnpRad.sh -r a_fof.txt -S rconnector-v1.2.0-Source
The absolute …
-
I have been assessing nucleotide diversity in a species of conifer and recently was able to recall invariant sites to be used in pixy. I ran pixy using a number of different parameters, such as arbitr…
-
**Describe the bug**
When trying to convert a vcf file with `genomic_converter`, it fails with this error:
```
################################################################################
##…
-
Hi Clément,
I used dnaPipeTE on both penguin RADseq and WGS data and I'm trying to understand the Counts.txt output. I would like to know the difference between "others" and "na" classes.
I also did…
-
Hi!
I'm running Ipyrad [v.0.9.81] and I'm having problems with step 7.
When I run the software without reference (de novo) it works fine.
But now i'm trying to do it using a genome of reference an…
-
Previous correspondence:
**Sandra** @sandrabohn
I've been wondering if we should start quality filtering the reads before we put them through the pipeline. What do y'all think about that?
**…
-
Hi again,
Why does the total number of observations (the sum of the frequency bins) in the projected DAF not correspond to the number of sites specified by the projection preview?
I've projected…
-
Hi, thanks for your software.
I have multiples samples and I did a population calling. Example of commands for 2 samples:
```
octopus --threads 1 -R ref.fasta -I sample1.sorted.bam -o sample1.…
-
Hi Issac,
I know this is not an issue for the easySFS program, and I thank you for creating it for the ease of applying it to dadi. I thought about posting this to ipyrad discussion, but i felt it …
-
Dear Gideon,
I'm trying to run conStruct with snps obtained using RADseq, I have 180 samples with 1249 loci and I got the following error:
"you have specified an invalid data partition "data" e…