Navonil De Sarkar

17 Questions 69 Answers 0 Followers

Questions related from Navonil De Sarkar

What would you do with C>T and G>T mutations from FFPE samples?(Deamination issues)

Its a cancer targeted panel, and these two are clearly two most prevalent observed mutations.

01 March 2016 8,696 4 View

Is there a tool?

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

04 September 2015 5,025 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...

19 August 2015 6,553 6 View

Can anyone provide a *.bed file human exome?

To be used in Genome MuSIC.

16 April 2014 1,192 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...

04 April 2014 8,733 3 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?

20 February 2014 2,439 10 View

Can any one suggest some document discussing the reason for mRNA degradation in stored RNA samples?

Expecting links for technical reports, papers, book link etc

10 December 2013 1,415 4 View

Any suggestions for a pipeline for calling variants from RNA-seq data?

Especially choice of aligner, different cut offs, whether to do duplicate removal cause RNA seq libraries are enzyme cut libraries, minimum depth of coverage for variant calling, rare allele...

10 December 2013 3,844 6 View

Can someone suggest the minimum concentration of total RNA that would be acceptable for any expression study using rtPCR?

Please share your experiences

30 July 2013 331 1 View

Need suggestions for expression database

Head and neck miRNA and mRNA expression deregulation database. Aware of TCGA. Want know about others.

12 July 2013 5,153 2 View

NGS sequencing issue: When the regerence genome is circular.

Aligner like BWA consider it a straightened reference, starting from 0 and ending at the end coordinate. Now the issue is with the reads which are starting from some tail ending coordinate and...

18 April 2013 4,435 8 View

NGS validation.

What should be the platform of your choice, if you are doing somatic mutation study, using ION platform

28 March 2013 4,695 4 View

RNA isolation protocol from Serum/Plasma

I need a suggession for a good RNA isolation protocol from Serum/Plasma. Looking for any kit name of any modification of protocol etc

05 February 2013 1,319 12 View

Methylation study issue

Is there any direct method of studing methylation. Is there any modified nucleotide which can bind specifically to methylated Nucleotide? Do not want to do bisulfide sequencing. Is there any other...

01 January 2013 5,536 2 View

DeNovo Assembly

Num. reads assembled: 1669184 Avg. total coverage: 16.60 Number of contigs: 13991 Largest contig: 112360 N50 contig size: 1171 that is the summary I got out of a de novo assembly (ion torrent...

04 December 2012 2,594 12 View

If I find sequence any gene (SNP) is under recent positive selection using extended haplotype homozygosity (EHH) or integrated haplotype score (iHS), what does that signify?

I got little bit of idea about this, but am looking for detailed insight.

13 September 2012 3,489 2 View

Which is the best protocol for mitochondrial DNA enrichment?

Is it organelle precipitation and then isolation or total DNA isolation and then enrich the target?

11 September 2012 3,724 7 View