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Questions related to Next Generation Sequencing
We have been using the QIAmp DNA Stool kit to extract total DNA from the gut of the Solea senegalensis larvae (2 dph to 60 dph), but when we do the amplification of the 16S RNA variable regions we...
02 August 2018 8,363 3 View
Leadership in Nepal: Genealogy of Discourse since 1990
30 July 2018 9,911 5 View
Is anyone familiar with BioMercator software? I want to construct a consmap but the QTL map. But when I input the genetical map and QTL map and try to combine them together, they will always...
26 July 2018 9,417 1 View
I am trying to isolate cfDNA from plasma samples (2-3 ml) for NGS. I get around 15 ng/ul concentrations of cfDNA from nanodrop but 10 times lower conc (1.4 ng/ul) from qubit dsDNA HS assay. Why...
23 July 2018 7,322 3 View
To calculate the statistical quantities like variance or mean expression of a gene across cells, it is unfair to compare expression counts of a say gene A, if we know different cells has not be...
15 July 2018 10,155 2 View
We've found that a PSD anti-rabbit and C1qa anti-rabbit give us the best images in conjunction with goat anti rabbit secondaries and a NGS block, but have been unable to stain for these...
10 July 2018 4,628 3 View
Hello everyone, I would like to have your advise on the choice of a method. I want to investigate fish gut functional diversity (not the taxonomic diversity). I know that GeoChip is good for...
07 July 2018 2,972 4 View
Recently, I have sequenced few samples (seawater source) using Illumina MiSeq platform and good quality sequences (70,000-1,20,000) are taxonomically assigned using QUIIME software pipeline....
12 June 2018 3,697 13 View
Hello, I understand there's disagreement regarding the similarity threshold for fungal OTUs, be it 95%, 97%, or 90-99%. In the literature, anyone of these threshold may be cast as adequate or too...
02 June 2018 3,559 4 View
both concepts relate to Genealogy ?
22 May 2018 9,751 1 View
It is utmost importance to understand the microbiome profile associated with genetic disorders. I studied the composition and function of microbiome profile associated with OSCC tissues compared...
15 May 2018 5,174 3 View
We have isolated metagenome from seawater. The whole metagenome was sequenced using NGS platform. The sequencing reads were assembled and whole metageomic sequence obtained. Genes were predicted...
11 May 2018 4,005 4 View
The website for the web interface for the genealogical sorting index (gsi) is down, and it seems hard to find the r-package as well. Therefore I need an alternative. What do you suggest? I need to...
03 May 2018 8,808 2 View
Hello everyone, I have a DNA sample that has been purified from FFPE tissue using the QIAmp DNA FFPE Tissue kit. I obtained a total amount of 1,5 ng of purified DNA, measured with NanoDrop: too...
28 April 2018 2,071 4 View
A. Positive history of refractive surgery B. Positive family history of glaucoma C. Positive history of halos around lights D. Positive history of brow aches E. Positive history of episodes of...
26 April 2018 3,765 1 View
I am new in NGS. For my research I need to choose a technique between MiSeq and HiSeq. I have 100 mouse fecal samples. I was planning to do the MiSeq but it's not fast as HiSeq. On the other hand...
25 April 2018 9,088 5 View
Hi everyone! I have a phylogenetic tree obtained using BEAST2 and inferred from two genes (COI and 18S). I would like to use this tree to improve my understanding of the evolution of each of the...
22 April 2018 4,490 4 View
I'm trying to extract DNA from tomato fruit in order to study the bacterial microbiota found inside the fruit using NGS. I have tried using a CTAB protocol, but the precipitate is highly charged...
21 April 2018 548 3 View
Planning to start some transcriptome and mutation analysis and I just need some recommendations on what the best NGS machine/technique for my needs would be.
11 April 2018 1,798 2 View
In brief, I have been labeling my cells with 50uM BrdU over >2X the doubling time of the cells. Thereafter, I would wash the cells 4X with 1XPBS before fixing them with 4%PFA. The cells are...
11 April 2018 2,359 2 View
F: 50 -CTKTTGGGYYCCCKGRYYG-30 Rev: 50-CGCGTCCACTMTCCAGTTCTC-30 These are primers for NGS sequencing of bifidobacteria from a publication. If you substitute, for example K, with G or T then...
10 April 2018 6,506 3 View
I'm looking for a formula that calculates minimum coverage needed to call a variant allele with a certain condifence level, given expected variant allele frequency (VAF) (or percentage of mutants...
06 April 2018 9,491 1 View
Hello, I'm following Thermofisher's "Ion 16S Metagenomics Kit User Guide", and I want to ligate Ion P1 Adaptors, and an Ion Xpress Barcode onto dsDNA amplicons for ion torrent sequencing (p. 16,...
30 March 2018 2,145 2 View
We have a biological condition that we believe decreases splicing fidelity in c elegans. In our preliminary RNA seq data using 2x50 bp, 22 million reads per sample and 5 replicates, we found only...
29 March 2018 3,323 3 View