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 anyone provide a *.bed file human exome?

To be used in Genome MuSIC.

03 April 2014 222 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 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

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

MGL tools

20 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

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Resistor definition in Piezoelectric bimorph with ANSYS workbench

Hello, good day! I am trying to simulate similar bimorph piezoelectric harvester with below commands. However, the output power doesn't change with resistor value. Please help to find the reason. ET,10,CIRCU94,0 !SET UP RESISTOR R,1,100000 !RESISTANCE VALUE TYPE,10 !SET ELEMENT TYPE E,1,2 !CREATE RESISTOR BETWEEN NODES 1 AND 2 Thanks in advance Regards,

02 March 2021 0 0 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Gel electrophoresis result for total RNA samples, 1.5 Agarose gel was used, How to improve the integrity of RNA?

Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue

02 March 2021 5,433 5 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Why does two different bioinformatics tools for the same proteins show different subcellular localizations?

During a computational analysis, I found that for a protein of a plant, two different subcellular localizations are seen using CELLO and WoLF PSORT. For example, in CELLO, it identified the...

01 March 2021 6,729 2 View