Is there a tool?

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

08 September 2015 4,851 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 7,176 6 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 4,932 3 View

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

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

03 April 2014 2,208 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 1,762 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 3,384 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 9,151 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 2,505 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 819 2 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

11 December 2013 3,364 5 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MGL tools

20 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View