dDocent User Help Forum

Good day all, I am trying to run dDocent v2.9.4 on MacOS 14.4 and am running into this error: /Users/

Let me add a detail: The dDocent_mail.log states the following: mawk: cannot open "mapped.1022.

Deal All I want to filter loci based on SNPS, According to pipeline (perl rad_haplotyper.pl script),

That looks to have fixed the problem, thanks! On Friday, September 29, 2023 at 7:34:59 AM UTC-6 Jon

I have vcf file with my ddrad data. I want to extract a handful of the loci for the skyline plot

Hi everyone, I am new to bioinformatics and job submission. I have been stuck trying to debug the

Hi, I followed the conda install instructions for dDocent on a 'normal' Linux systemm (no HPC

Hi all, I realized that I need to extract the fasta sequences flanking some of my SNPs (the outliers)

Also, see note here: https://github.com/jpuritz/dDocent#if-you-are-getting-samtools-errors On Thu,

Hi Paige, It's not documented, but it is fully functional here (https://github.com/The-Eastern-

Hello Santosh, I'm a relatively new user of dDocent and I've been having a few problems with

Hello, we have identified several hunderd of high-quality SNPs from MIG-Seq data of various fruit

Hmm, having a similar problem, does not look like recent posts on here have gotten many responses,

Hello - I have ~1400 samples to run across multiple (60) populations. Best estimate is 32 days of

The lab that generated the dataset said that " We noticed some regions got enormous number of

I've answered my own question. There's a handy python script that does the job: https://

Dear Jon and others, I have a question about why dDOcent requires paried-end (PE) reads for de novo

Hello, I started a new conversation about this issue because this is older. Sorry if that wasn't

In the SNP filtering tutorial, both mac and maf (minor allele count and minor allele frequency) are

For the subset, no trimming is needed to create the optimized assembly using the parameters you got

Hi Pearce, There's a lot to unpack here. First, that's an old version of dDocent, please have

They are in the dDocent.runs file Jon Puritz, PhD Assistant Professor Department of Biological

Hi Russel, This is really difficult for me to estimate for you. I would suggest though, not starting

Thank you Jon! I will try both suggestions! Am Mittwoch, 3. März 2021 16:54:08 UTC+1 schrieb the...@

Hi Josh, Again, this is going to depend on your samples, both number and coverage level. From you

Dear All, Could you please suggest me how can I solve it? help please $ vcftools --vcf ZZ_ZW_BiSnps.

Any line with a freebayes command, so yes 489 and 507. For STRUCTURE, the best practice would be to

My gut feeling is this has to due with weird characters introduced by NCBI. I would double check that

Hi Tereza, Yes, you should be able to simply concatenate them something like: cat *.fna >

For debugging or troubleshooting, please include the following information: The last output in