What is the best way to make an in-house database with allele frequency ?

Hi, I am currently working on making a variants database. I generate seperate VCF files for each samples them and merge them using VCFtools (using mergeVCF command) to make a multisample VCF...

31 December 2017 8,185 6 View

Sambamba-sort problem (not enough data in stream) ?

Hello, I'm getting an error: "sambamba-view: not enough data in stream" by running sambamba-sort, below my script : PS: I get this error only for some bam files but for all !! "sambamba view -t...

01 February 2017 4,910 0 View

How to create a test predictor with the genotype case/control study (genetic association) ?

Hello,I have a Case / Control genotype study (one qualitative phenotype). so I carried a genetic association analysis with PLINK (logistic) and I've identified hundreds of SNPs with very low Pval...

07 August 2016 1,404 4 View

How to calculate Gene-Gene Pearson correlation ?

31 December 2015 7,063 13 View

What option do you usually use with featureCounts to have count according to isoform ?

09 October 2015 5,000 1 View

How can I make a Polytomous analysis to define clusters in RNA-seq count data?

03 April 2015 5,340 3 View

How can I calculate the average values in dataframe with R?

I have a dataframe with a first column contains the gene symbol and the others column contains an expression values. the Column of symbol can contain the same symbol more then one time. So I would...

02 March 2015 1,980 5 View

How can I do clustering with RNA-Seq data ?

I have Cuffdiff (--no-diff) output tables and I want to perform clustering : 1) better to use Count or FPKM ? 2) Are "standard" clustering algorithms appropriate for RNA-Seq data due to its...

02 March 2015 7,399 23 View

Is there a tool for converting a variable step wig to a fixed step wig?

01 February 2015 888 5 View

How can one convert a nucleotide-space to a color-space format ?

Does anybody know where I could find a tool to convert a nucleotide-space sequence to a color-space sequence? Thanks a lot in advance,

10 November 2014 4,041 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