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Questions related to Next Generation Sequencing
Hi all, I am using IDT capture probe to enrich the target region of tumor samples for sequencing. However, I found Skewed GC bias in NGS data, which resulted in poor capture uniformity and lower...
10 February 2020 3,604 2 View
Our project objective is to investigate the genetic diversity of Palestinian date palm, cultivars. 6 primers were ordered, these primers were designed specifically for NGS analysis. DNA was...
07 February 2020 813 2 View
A NGS panel of truseq was performed, the SNP expected of CSN1S2, Ch 6, Position 87266177 are C/T, but we received A/G. There is an explain about that?
29 January 2020 1,219 2 View
Dear all, Currently, I am processing a NGS data using cutadapt to remove 3p and 5p adapter sequences from reads. Normally, as I notice, the percentage of trimmed reads (reads with removed...
10 January 2020 8,334 3 View
Hi All, we have a bioinformatics challenge and we would love any help this community can offer. We have data from a target-enrichment experiment that was supposed to capture certain...
10 January 2020 1,004 3 View
I have a problem with adapters dimmers to perform an NGS. I would like to know how the best way to separate my library from the contaminant dimer. My library has approximately 200 bp and the...
22 November 2019 2,538 4 View
Hi All I start sing the software STAMP, My project is to compare two gut microbiota groups. I need to know what is the significant different between this tow group in family level. could you...
18 November 2019 2,728 2 View
Hello everybody! I need to perform new experiment. I want to stain collagen fibers in porcine tissue by means of mouse primary antibody. Then to visualize it I am going to use anti-mouse goat...
10 November 2019 2,543 2 View
There is a task to identify rapidly current variants of potyviruses in potato and tomato plants. What would yo recommend - NGS or Sanger method to make it faster? If NGS, what method shell we use...
07 October 2019 9,602 2 View
Dear all, I want to use cutadapt when processing NGS data in order to remove 4 nucleotides at both 3-end and 5-end of each read. Could you suggest a command that I can use to achieve this purpose?...
24 September 2019 4,566 2 View
I want to isolate DNA and RNA from feline faecal samples in order to determine which pathogens (viruses, bacteria, fungi, parasites...) are present in the samples. The isolation will not be...
23 September 2019 3,148 4 View
Dear All, could some please suggest proper PhiX concentration for multiplex Illumina sequencing with use of MiSeq kit v2 and Nextera XT. samples #1-11 are highly similar - around 50-56%GC sample...
08 September 2019 2,934 1 View
I would like to do next generation sequencing on cells sorted based on an intracellular stain. Is there a best practice for how to fix the cells such that my sequencing run is not compromise?
29 August 2019 7,893 2 View
Is q-PCR sensitive to Pseudogenes?
16 August 2019 2,970 2 View
Since I m new to NGS, I have this basic doubt. Kindly pour your knowledge on this regard.
06 August 2019 4,010 3 View
Hi, I have an isolated species from environmental samples, what is the best way to identify it? I think using Sanger sequencing with total 16S will be enough, but I heard that NGS (shotgun method...
17 July 2019 7,386 6 View
I´ve been searching for controls in NGS but I´ve only find quality controls. So I´m in doubt if it isn't necessary the positive and negative control during the sequencing. Hope someone can help me
10 July 2019 7,473 1 View
Hi, I'm doing an analysis of the immuno repertoire en T cell from different patients and this in several conditions. How could I compare two sets of TCR sequences (each set are arround 100 000...
08 July 2019 1,418 7 View
I am trying to amplify two genes, each ~2kb in length. I am looking for ways to do this at the stages of cDNA synthesis and PCR amplification. Primer design and thermocycle specifications do not...
13 June 2019 2,400 1 View
I have NGS data of TCR-a from probiotic and control group. I want to see if there are identical sequences between these 2 group. In order to do that, I want to find out what are these identical...
01 June 2019 7,844 6 View
Hello everyone, I was dealing with library construction for low complexity region from human genome, And I also found that, the sequencing depth are obviously bias: which means, some reads were...
07 May 2019 3,616 11 View
I am doing a project on trying to stain and image the neuromuscular junctions of drosophila leg muscles in great detail (with the possibility of imaging the boutons as well). So I have got two...
06 May 2019 5,696 4 View
I am validating the screening of BRCA1 and BRCA2 genes by NGS (Ion Torrent). I would like to have more samples with pathogenic variants to compare with my samples and to confirm my validation...
22 April 2019 2,144 3 View
I'm planning on a gene expression analysis study of mosquito midgut in response to a virus. I want to know how long it will take for gene expression analysis using next generation sequencing. Or...
22 April 2019 8,515 3 View