How to count number of overlapping reads of RNA seq?

I have big wig file of RNA seq and BS seq data.I want to calculate number of overlapping reads of RNA seq that covers the methylated CG. Which function should I use to count number of overlapps

03 April 2016 9,795 2 View

Pandas in python?

03 April 2016 6,700 1 View

Low enrichment with lots of background in encode control?

02 March 2016 6,931 0 View

Analysing 20,000 histograms in R?

02 March 2016 3,338 1 View

RNA Sequncing sample selection?

I have 100 RN A seq samples and i have mapped them using tophat. but the alignmnet is so so. like given below: Left reads: Input : 24818 Mapped : 1562 ( 6.3% of input) of these: 122 ( 7.8%) have...

02 March 2016 7,723 4 View

RNA sequencing data?

I have RNA seq data which I have mapped using tophat. but the alignmnet of these sequences is very poor . How many aligned reads should be there for selection of RNA sequneces.can it be more than...

02 March 2016 9,579 5 View

Tophat output directory issue?

I want to get the output of tophat in a new directory each time instead of its by default directory ./tophat_out. For this i have also added to tohat command -o directory_name but every time it...

02 March 2016 139 5 View

I have RNA sequencing files and i want to check the gene expression of all genes from that file. Can anyone help?

I have RNA sequencing files and i want to check the gene expression of all genes from that file? I want to know how can i get genes from that rna sequence files? Although it is a basic question...

02 March 2016 5,694 5 View

MAking a table in R?

I want to gather methylation column from 100s of BS sequences files into a single file in a way that the first column should be the name of genes and the other 100 columns are the methylation...

02 March 2016 5,862 3 View

Tophat output?

I have tophat out put and i have to find "The number of aligned reads whose mate pair was also aligned to the reference." from which file i can find this information as the align_summary.txt...

02 March 2016 6,894 0 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