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Questions related to Next Generation Sequencing
I extracted viral RNA samples using Qiagen Viral RNA kit. the samples gave concentrations average 30 ng/ul and purity of average 2 for both 260/280 and 260/230. I shipped the samples using RNA...
21 October 2018 1,982 5 View
454 GS FLX Titanium system which is capable of generating 700 megabase (Mb) of sequence in 700 bp reads. MiSeq reagents enable up to 15 Gb of output with 25 million sequencing reads and 2 ×...
18 October 2018 2,345 3 View
Next generation sequencing (NGS) is a wonderful tool for identifying waterborne pathogens. But I was wondering what are the challenges we face in NGS in terms of identifying the correct pathogen...
11 October 2018 455 2 View
I'll preface this by saying our NGS Core facility handles most of our analysis. So perhaps in my limited understanding of the analysis workflow, I'm not correctly articulating what I'm looking to...
27 September 2018 10,069 4 View
So I am trying to proof that a specific TF binds to my gene. I have done this by ChIP. Worked all fine. Now I wanted to delete the TF binding site via CRISPR/Cas9. Unfortunately (and i have...
24 September 2018 2,470 6 View
If I am interested in a customized mRNA-only Sequencing (RNA-Seq) based on few transcripts (not the whole transcriptome), and after having satisfied & permissible RIN values for my extracted...
22 September 2018 1,885 3 View
Hi everyone, Can I use the NGS method to study the effect of a bacterial secondary metabolites on wheat? Do you have a reference article? Thankful,
22 September 2018 1,127 3 View
Please mention in details the advantage and disadvantage of any particular software if you recommend. Thanks in advance.
12 September 2018 8,480 6 View
Any tool or package to prepare input files for Circos visualization of NGS data? I know of some, but not very user-friendly.
11 September 2018 652 2 View
Hello, I am looking for a company or a lab that creates T-cell lines with specific mutations? Does anyone know where I can find such a thing? I am trying to find ones with mutations in...
05 September 2018 9,097 1 View
Hi We've just started using the Illumina Next-Seq platform and haven't been getting good results sequencing our CEL-Seq2 library (75cycle, R1=15bp, R2=77bp), as opposed to what we've been getting...
24 August 2018 7,589 7 View
Next Generation Sequencing techniques are currently used in microbial profiling and other studies. Between the NGS (specifically Illumina Miseq Technique) and PLFA, which is the best method to...
23 August 2018 2,329 3 View
Is there any other software to plot TADs ( I have chromosome start and end position), normalized tag count from ChIP-Seq data, and log2FC of genes (fold change from RNA seq data) in one graph?
09 August 2018 1,154 1 View
Apart from amplification requirements being mandatory for NGS, what are the other differences or advantages third generation sequencers like Oxford nanopore and PacBio provides? Which one is more...
07 August 2018 6,012 3 View
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 8,329 3 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 9,406 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 7,289 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 10,113 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 4,610 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 2,963 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 3,671 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 3,528 4 View
both concepts relate to Genealogy ?
22 May 2018 9,735 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 5,160 3 View