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

Promoter file duplicated entries?

NM_001081462 chr5 134833230 134833830 0 - 12.5NM_001081463 chr5 134833230 134833830 0 - 12.5NM_001081464 chr5 134833230 134833830 0 - 12.5NM_001081465 chr5 134833230 134833830 0 - 12.5NM_001081466...

02 March 2016 2,098 1 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

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

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

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

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

What is the characteristic length to determine the Reynolds number for the scattered turbulent fluid flow?

Dear all, I just saw this example in FB on the difference between laminar flow and turbulent flow. The flow from a pipe hits the sink and scattered. The flow from the pipe is characterized as...

02 March 2021 1,999 5 View