Hi everyone,
I am planning a ddRADseq experiment with non-model plants (this means, no reference genome available), and I am wondering how...
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Calculate number of reads per sample for ddRADseq
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Calculate number of reads per sample for ddRADseq
Hi everyone,
I am planning a ddRADseq experiment with non-model plants (this means, no reference genome available), and I am wondering how... -
Comparing loci across catalogs
Hi all,
Context: I'm using the Stacks (v2.59) ref_map.pl command to analyze garden and wild samples of my species, and have aligned my... -
Introductions: NGS and RADseq Analysis
Hello all! Firstly, thanks to the developers, administrators, and participants of SeqAnswers for providing insight to questions and keeping this site... -
mapping hundreds of RADseq fastqs to ref genome.
I would like to map hundreds of fastq.gz single-end RADseq files to a single reference genome.
But, bwa mem is making a map file (.sam)... -
RADseq library Prep- Newer protocols for pooled samples?
Hello All,
I am hoping to use RAD-seq for the discovery of SNPs for a population genomics investigation. I have a few questions related... -
PCR-free ddRADseq?
Hi all.
I'm helping out on a RAD-seq project and we're exploring different options to assess population structure for several hundred... -
Spitballin': PCR-free ddRADseq?
Hi all.
I'm helping out on a RAD-seq project and we're exploring different options to assess population structure for several hundred... -
Beads cleanup after enzyme digestion in RADseq: Yes or no?
Hi all,
I am working on double digest RAD sequencing, and I have quite a general question. In the ddRAD protocol of Peterson et al. they... -
Really Low Bowtie2 Alignment Numbers From Demultiplex in STACKS
In STACKS, I ran process_radtags and get close to 20 million reads. They are paired-end 150bp reads.
/home/srile14/stacks-1.48/process_radtags... -
Optimizing a ddRADSeq study with a large genome
I am designing a study to investigate the population genetic structure of an endangered species. We've decided to go the ddRADSeq route, and I have a... -
ddRADSeq Libraries
We seem to be having some difficulties creating reproducible ddRADSeq libraries.
We are noticing that after running the first of the processing... -
Questions about RADseq oligo
I will be genotpying ~500 samples using the original RADseq protocol, and I have a couple of questions.
First, is desalting a sufficient... -
Need feedback on RADseq using enzyme BbvCI
I am planning to genotype ~520 samples using original RADseq (Etter et al. 2011). The project has 2 goals: (1) construct a linkage map using a subset... -
Shearing digested DNA for RADseq
Hello,
I am making libraries for RADseq. I am trying out the Covaris ME220 for shearing the digested DNA. The shearing seems to be highly...
