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Questions related to Next Generation Sequencing
To all the brilliant scientists and lab techs out there, I am preparing DNA library for NGS illumina, using SPRI beads purification method. My input gDNA is 500 ng. I've recently noticed that my...
14 February 2018 5,558 3 View
I am checking different software to do the scaffolding of metagenomics assemblies. Despite some assemblers such as metaSPAdes already perform the scaffolding, I would like to verify the...
11 February 2018 8,799 2 View
Searching tips to effectively sequence poor quality/quantity bacterial DNA using Miseq NGS. One of my earlier experiment involving starting concentration of 165ng/mL of bacterial DNA yielded an...
07 February 2018 1,850 3 View
We sequenced embryos for aneuploidy screening, and also for control took one genomic DNA sample, previously known with normal karyotype. All the samples were amplified with SurePlex system. After...
02 February 2018 1,987 1 View
Hi, I carried out a NGS analysis(resequencing). I got variant calling data and raw data(fastq). I convert fastq file to fasta file and opened with text reader program. What I found was about...
30 January 2018 5,212 2 View
I am new to bioinformatic analysis of nucleotide sequences. I have several NGS nucleotide sequences (virus) coming from patients, that i need to align and perform a phylogenetic analysis. I would...
25 January 2018 6,760 3 View
Hello, for routine work, we are using the QIAamp DNA Mini Kit to isolate the DNA from bacteria. This kit works fine when the intention is to use the DNA for routine PCR. However, the yield is...
24 January 2018 8,373 4 View
Hi! We are planning to assess DNA methylation profile of 100-200 cells using bisulfite sequencing on the NextSeq500 instrument. However, the kits designed for single cells (Accel-NGS® Methyl-Seq...
23 January 2018 4,208 3 View
We have designed RT-PCR Primers based on CDSs predicted from NGS data with confirmed protein similarity of various NCBI protein data bases. Our predicted CDSs are not less than 100 AA. However,...
22 January 2018 5,265 3 View
I am working on GWAS and planning to use chromopainter, finestructure and globetrotter from plink. I am trying to convert plink 1/2 file format to chromopainter file by using the...
20 January 2018 8,707 2 View
I'm trying to use Bcl2Fastq to convert raw BCL files into fastq files from a paired-end targeted sequencing run on an Illumina MiSeq. I'm able to run Bcl2fastq in a linux server environment...
17 January 2018 4,818 2 View
Does anyone know how to access or download exonhunter? I've found a URL from the research group's publication http://www.bioinformatics.uwaterloo.ca/downloads/exonhunter but this is seems not working.
15 January 2018 7,483 3 View
Hii, Greeting Everyone Currently i am working on Next Generation Sequencing, will anyone suggest me the depth/coverage needed for a sequence obtained through any platform of NGS particularly...
11 January 2018 4,379 5 View
Which one is the best tool for predicting both gain-of-function and loss-of-function mutations if you have to select only one server from PolyPhen and SIFT?
08 January 2018 779 5 View
Hi everyone, I am trying to do some methylation analysis (human DNA, NGS) and I've come across several alternatives. All of them need to fragmentate the input DNA. Some make use of sonication...
04 January 2018 4,518 1 View
Dear All, Would you suggest to maintain or remove duplicate reads when studying viral subpopulation (e.g. SNP) by NGS? I think that both approaches can bias the results...but I can not figure out...
19 December 2017 9,703 2 View
I have faced this with more than one gene. in the step of gene annotation of my NGS data I found in many case my enzyme of interest but I found that this enzyme is found in multispecies, it means...
09 December 2017 2,732 1 View
Nanopore MinION produces .fast5 files as raw data. How to convert .fast5 file into fastq format?
07 December 2017 9,695 4 View
I wanted to compare the result of next-generation sequencing of a case study with TCGA, please anyone has idea how ?thank you
02 December 2017 2,761 2 View
In a typical ddRad protocol we bring samples to a similar concentration before multiplexing and sequencing. However, I was wondering if two different genomes from 2 species (e.g. c-value of 1.8...
28 November 2017 3,710 3 View
what ca we do if we are sure that one of 100 of bacteria has desired gene (which we have its DNA sequence) and we want to know which one has it? to explain more: I have sequenced 100 fosmid with...
27 November 2017 5,998 4 View
Hello, my question is more directed to those who have experience in treating sequencing data: alignment and phylogenetic tree construction. I have ratovirus sequences coming for NGS (clean...
20 November 2017 9,993 2 View
hi all, anyone has some advices considering bacterial genome assembly with use of Unicycler (@Galaxy)? I am trying to assemble paired-end data obtained from Illumina platform. Data was...
09 November 2017 3,813 4 View
I have applied my SAM file from somatic exome data on HaplotypeCaller software and it has generate a VCF file contain multiple SNPs and Indels. Is this software just for haploid cells?
08 November 2017 7,572 1 View