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Questions related to Next Generation Sequencing
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 3,994 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 8,785 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 2,054 4 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 9,056 5 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 515 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 1,781 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 6,470 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 9,465 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 2,121 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 3,288 3 View
excuse me for that as recently joined this field and trying to make my way. I have a data set of 1545 SNP markers from NGS for many traits of 63 individuals (F2 intercross) the genotypes analyzed...
29 March 2018 7,990 4 View
The NGS data (VCF files) contain the variants from all the transcripts for a particular gene. Which is the best site/tool to filter out all the non-primary transcripts.
29 March 2018 7,900 5 View
I am currently performing IHC for human tissue microarrays but all my tissues, including negative control where I did not add any primary antibody, stained positive. I block peroxidase with H2O2...
23 March 2018 5,134 5 View
I’m trying to figure out how many samples per run I can sequence on various platforms for shot-gun metagenome sequencing. I’ve read that 100-150 Gbytes per sample are recommended for WGS of human...
21 March 2018 7,751 4 View
I'm trying to generate a smaller fragment of 16S from a water sample, so it can be NGS amplicon sequenced. The limit of that service is about 500bp.
15 March 2018 8,119 2 View
Hi, I'm searching for methods to validate somatic mutations in pancreatic beta cells. The mutations are found by Next Generation Sequencing and I have try Sanger Sequencing with no results.
13 March 2018 1,878 5 View
I am very much interested for illumina sequencing of 16S rRNA gene of gut microbiota.
11 March 2018 9,092 4 View
We recently sequenced 96 samples on a Nextseq, prepare from single- and double stranded DNA, using the appropriate protocols. Turns out that the samples using the single-stranded protocol...
01 March 2018 8,504 2 View
I am currently looking into intron and if mutations at the 3' end of an intron are likely to cause a splicing defect. I have not way of experimentally validating this.
26 February 2018 1,411 3 View
I have obtained 12 different FASTQ archives from NGS sequencing, after taxonomical OTUs assignation of the archaea sequences...anyone knows how to make community comparisons among them? Thanks...
23 February 2018 9,326 2 View
NGS for Gut Microbiotal Analysis
22 February 2018 9,654 3 View
I have basic knowledge for nucleotide sequence analysis and gene annotation. I am looking forward for certification course which would give an insight into NGS technology, alignment of reads...
20 February 2018 3,975 3 View
Would appreciate any hints/information about submission of NGS data to public databases. In short – manuscript, describing abundance (in percent) of particular microbial groups in different...
19 February 2018 632 5 View
I want to analyze fusion transcripts of my RNA-seq data. I have used EricScript (https://sourceforge.net/projects/ericscript/) tool which has detected several fused transcripts. Now I don't know...
16 February 2018 1,673 1 View