Bilgenur Baloglu

10 Questions 22 Answers 0 Followers

Questions related from Bilgenur Baloglu

Does anyone have any idea why Polynucleotide kinase (PNK) phosphorylation of primers may fail?

I am trying to phosphorylate both of my forward and reverse primers prior to the PCR. Primers that are 5' phosphorylated (theoretically) do not affect PCR since primer extension occurs from the...

09 December 2018 6,587 9 View

How can one randomly select a subset of ecological community data and compare their similarity to each other?

Dear all, I am working on an ecological community species data matrix (site by species), and I have many species and sites. I want to select sub-communities with different sample sizes randomly,...

27 January 2017 9,059 3 View

What is the best way of analyzing spatial and temporal variation in species composition and abundance dataset?

I have 4 sites with a total of 22 species (i.e. site1 has 7 species, site 2 has 15, etc.). I also have multiple weeks’ species abundance data for each site. I want to analyze the species diversity...

09 May 2016 4,579 3 View

How can I fit rarefaction curves?

To determine whether the sampling was sufficient, I plotted rarefaction curves for four sites using rarecurve() function in R vegan package. Seems like the curves have not yet "converged" (i.e....

22 November 2015 1,663 2 View

How can I decide the read count threshold when analyzing NGS data?

I am working on paired-end Illumina NGS data, and the steps go like this: Assembly, demultiplexing, and the downstream data processing. Coverage (aka total read counts) is an important parameter...

24 March 2015 4,644 5 View

How can I troubleshoot with high absorbance at 230 nm (260:230 is 1:2) for a DNA extract?

I am experiencing a contamination problem in my DNA extracts. I did DNA extraction from water samples using phenol/chloroform. However, I do get a shoulder/high peak at 230 nm whereas there is a...

24 October 2014 7,767 5 View

How does one join two text files with using their shared sequence identifier?

I am working on Sequence Read Archive (SRA) datasets. I have one fasta file containing the SRA identifier and the sequence (atcagtt..) and one blast output file including sequence identifier, gi...

01 September 2014 4,345 11 View

How can I extract random lines from a text file using a command line?

I have an excel file which contains the lines I want to extract from the original file. There are a few issues: 1) that I do not have standardized lines aka identifiers. So I cannot use a command...

15 July 2014 6,110 22 View

Which equipment is the best for deep water sampling?

I will need to do deep water sampling (preferably at different depths with some number of replicates) firstly in lake and reservoirs and then in marine water. I am currently looking for deep water...

02 April 2014 3,705 3 View

Can anyone suggest a tool to detect contamination in NCBI Illumina high-seq transcriptome databases?

I know that there are several approaches to detect contamination in submitted NCBI transcriptome studies databases, but since I am doing a literature review, I would appreciate if you add up to my...

09 March 2014 7,811 2 View