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Questions related from Bilgenur Baloglu
I do rolling circle amplification (RCA) on my ligated PCR products prior to Nanopore sequencing. After using enzymatic and mechanical (covaris g-tube) fragmentation of the RCA products, my...
03 March 2019 2,548 3 View
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...
12 December 2018 7,530 7 View
12 December 2018 9,016 1 View
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...
05 May 2016 9,090 4 View
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....
11 November 2015 5,334 3 View
So far I used VennDiagram and venneuler packages of R, but the main thing with these two packages is that they do not generate a proportional diagram. Lets say one set has 25 elements (A) and the...
09 September 2015 6,251 5 View
I have large-sized (~8-10 GB) trimmed paired-end datasets (separated into two single files). I installed a local blast on a linux environment, and am planning to do nucleotide alignments with a...
03 March 2015 5,611 12 View
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...
10 October 2014 9,905 6 View
I am working on environmental DNA (eDNA) in aquatic environments. As mentioned by Barnes et al. (2014), environmental conditions influence eDNA stability in aquatic systems. Recently, the eDNA...
10 October 2014 7,409 18 View
According to NCBI Blast tutorial, e-value indicates the number of hits one can "expect" to see by chance when searching a database of a particular size. However, this definition is somewhat too...
10 October 2014 7,998 12 View
High sequencing depths provided by Next Generation Sequencing (NGS) technologies indicate an exponential increase in the volume of sequence data in the last decade, but it comes with a cost. Do...
08 August 2014 6,539 9 View
NCBI Genbank hosts enormous numbers of COI sequences. However, it is not explicit how many species have their COI being sequenced, since there is also so many multiple sequences from one single...
07 July 2014 9,949 7 View
I have a couple of transcriptomic sequences that were generated with different sequencing platforms such as Miseq and Hiseq. The output format is hence different than Sequence Read Archive NGS...
07 July 2014 10,019 12 View
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...
07 July 2014 3,743 23 View
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...
04 April 2014 8,380 4 View
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...
03 March 2014 3,198 2 View
I need a program to analyze Illumina transcriptome data. CLC has a free-trial but that only lasts for 14 days. I would like to have a program set up on my personal computer, so that I can analyze...
12 December 2013 5,814 8 View
