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Questions related to Next Generation Sequencing
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 8,015 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 7,922 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 5,153 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 7,779 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 8,158 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 1,904 5 View
I am very much interested for illumina sequencing of 16S rRNA gene of gut microbiota.
11 March 2018 9,114 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 8,516 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 1,427 3 View
I am trying to map a mutation in an intron to see if it may cause splicing defects. I cannot validate this experimentally.
26 February 2018 6,204 0 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 9,352 2 View
NGS for Gut Microbiotal Analysis
22 February 2018 9,664 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 3,993 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 659 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 1,683 1 View
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 5,586 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 8,821 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 1,868 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 1,997 1 View
I have performed differential expressed genes (DEGs) using the DESeq2 package. I understood that this package has its own normalization method to calculate for DEGs. To represent the data on gene...
01 February 2018 9,900 2 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 5,231 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 6,772 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 8,410 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 4,233 3 View