Joshua A. Thia

12 Questions 26 Answers 0 Followers

Questions related from Joshua A. Thia

What tools can be used to analyse RAD haplotypes in pooled samples?

Hi all, I have pooled RAD-seq data (multiple individuals sequenced in a single library prep) and I am interested in haplotype frequencies. Reads have been mapped to a de novo reference and I have...

17 May 2017 3,265 3 View

[SOLVED] How do you export bootstrap node support in R's 'ape' package?

Hey all. Been getting a little bit more familiar with R's ape package for phylogenetic analysis. I am having a difficult time figuring out how to export the bootstrap node support with my tree. I...

20 July 2016 5,371 3 View

How do you remove mate reads mapped to different "chromosomes"?

I have created a denovo reference "genome" of RAD contigs and have mapped back my reads using BWA. Using the the samtools flagstat option I queried my read alignments. An example: 3232117 + 0 in...

04 April 2016 4,016 4 View

[SOLVED] What programs exist to remove FASTQ sequences based on prefix?

I have sequence data from the ezRAD method. Most of the sequences have the cut site "GATC" at the start, however some do not (see example below). I am trying to find a program that will remove any...

21 January 2016 3,520 1 View

[SOLVED] What's up with Ferretti et al. 2013 calculation of Fst from pooled NGS population data?

Hey everyone. Has anyone read the Mol Ecol paper by Ferretti et al. 2013: Population genomics from pool sequencing? Specifically, has anyone tried to use their calculation of Fst from estimated...

04 June 2015 8,082 4 View

Population genomics: are you able to "break up" mpileup files into individual populations?

I have analysed some pooled RAD-seq data, and there is a particular program I want to use but it requires (1) one population, and (2) only one chromosome, from a mpileup file. This is a bit of a...

11 May 2015 591 4 View

How do I estimate allele frequencies from pooled RADseq data?

So here is my problem: I've been reading the literature on RADseq to get population allele frequencies. I'm thinking of using pooled sampling for cost-efficiency. However, I can't seem to find any...

02 March 2015 169 10 View

Could someone please define what tm and ts outcrossing means? [SOLVED]

Could someone please provide me with a clear and simple explanation of what tm (multilocus outcrossing rate) and ts (single-locus outcrossing rate) are and how to interpret them. As I currently...

11 August 2013 6,953 6 View

Fruiting trees as "magnets" for secondary seed predators?

I am trying to track down research articles that address this question. More specifically, experiments that address the magnitude of secondary seed removal from under adult conspecifics that are...

29 June 2013 1,345 5 View

Removing PCR inhibitors POST-extraction?

I am working with plant tissue - specifically cambium - and have found that despite various methods (CTAB, modified CTAB, kits) I am still having issues with inhibitors/contaminants - which I...

23 May 2013 9,584 33 View

Have you thought about using DNA barcoding to discriminate between the morphologically similar sea-squirts Ciona savignyi and Ciona intestinalis?

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09 December 2012 4,290 4 View

How can I "clean up" organic compounds from a DNA extraction?

I have extracted DNA from the cambium of trees, but I am finding that I have high levels of protein and organic compound contamination (absorbance high at 230nm and 280nm on a spectrophotometer);...

07 November 2012 4,411 25 View