NGS validation. - FAQS.TIPS

More Navonil De Sarkar's questions See All

Is there a tool?

Is there a tool that can help me to identify chromosome and coordinate of mutations formatted...

08 September 2015 4,995 2 View

Why do I get a G>A mutation in my sequencing data?

If you see most of your relevant mutations G>A, what would you infer (generally) other than any sequencing error. Chances of sequencing errors are already addressed. Data generated on Prostate...

07 August 2015 7,324 6 View

Can anyone provide a *.bed file human exome?

To be used in Genome MuSIC.

03 April 2014 355 1 View

Can you suggest a P-value cutoff for a somatic variant call?

I am using fisher exact test to call for somatic mutation. Now, if I go for any multiple correction, it appears to me as overdone. It is removing almost everything. With, 0.01 cut off on and...

03 April 2014 5,085 3 View

Is there any restriction enzyme which can specifically cut a DNA strand sensing either a stretch of 8Cs or 8Gs?

03 April 2014 2,334 0 View

What should be the minimum depth of coverage for variant call?

For calling somatic several events could happen. One is LOH. For LOH what should be the minimum depth of coverage in the paired diseased tissue which is homozygous at this locus (blood is a...

02 March 2014 1,902 3 View

What should be the minimum read depth of a minor allele for a reliable variant call?

What should be the minimum read depth of a minor allele for a reliable variant call? I would be needing some journal reference in that respect. I would like to cite it as a support for the choice...

02 March 2014 3,539 8 View

EdgeR pipeline for a differential expression?

For a differential expression with CPM, what should be the fold change cutoff for considering the expression deregulated?

01 February 2014 9,402 11 View

VCF compare: Can anyone suggest an appropriate tool?

Job is to find somatic mutation from paired (GATK) VCFs from tumor and normals.

31 December 2013 2,645 2 View

Comparing VCFs for somatic mutations?

I need to compare VCFs for somatic mutations (paired samples), including snp, indel and LOH. Is there any tool other than Mutect that I can use?

31 December 2013 955 2 View

How to learn more about SPSS and its Application?

I would like to learn more about SPSS and Its application especially in regards to data analysis. Please suggest me how I can learn more about it. Thank you so much.

11 August 2024 9,101 4 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

Can you connect an HPLC to a Mass Spec only at a certain time point?

Can anyone explain this method? Especially the last statement where it says only at 1.5 to 2.5mins was the MS/MS connected to the UPLC. How is that possible, is it a feature in this specific...

11 August 2024 8,141 3 View

Baseline drift in HPLC? What causes this?

Hello, Why do i see this baseline drift when i compare my blank (black) to the sample (blue)? Any suggestions as to why this happened? Thank you!

11 August 2024 3,770 4 View

Text-Communication from the M1 Hand Area using BCI—and then there is Elon Musk?

Willett, Shenoy et al. (2021) have developed a brain computer interface (BCI) that used neural signal collected from the hand area of the motor cortex (area M1) of a paralyzed patient. The...

10 August 2024 7,180 0 View

Has anyone applied Python in the field of textile engineering for data analysis, automation, or smart textiles?

I'm currently exploring the application of Python in textile engineering, specifically in areas like data analysis, process automation, and the development of smart textiles. I'm interested in...

10 August 2024 7,429 2 View

How can I use the cif data obtained from rietveld refinement extracted via gsas2, for microstructural analysis using ETEX software?

09 August 2024 7,718 0 View

Is this a facetotecta nauplius?

This larva was captured using a plankton net in the Persian Gulf during the summer. I believe it may be a Facetotecta nauplius.

08 August 2024 3,746 4 View

How to confirm the site-directed mutagenesis result without performing NGS?

I'm cloning a fragment of 3200 nts into plasmid. The cloning was successful, however, 02 amino acids were mutated. Now I want to fix these 02 aa by site-directed mutagenesis technique using...

08 August 2024 4,645 2 View

May members post flyers about opportunities to present at a conference? If so, where to post?

May members post flyers about opportunities to present at a conferehttps://veraeducation.com/nce? If so, where to post for the Virginia Educational Research Association? https://veraeducation.com/

08 August 2024 4,585 1 View

Navonil De Sarkar

I really need some good suggessions... Thanks

Is there any option to check somatic variant, by the use any probe based technologies?

Xin Lu

I think you can use allele specific PCR, or if the mutant allele frequency is not too low even Sanger sequencing can give you a quick validation.

Jo Vandesompele

According to market study performed by Ghent University spin-off company pxlence, 56% of scientists (n=200) validate their NGS findings with Sanger sequencing. pxlence has PCR assays for the entire human exome.

https://www.pxlence.com