Are transcripts with class code X could possibly be the anti-sense RNA transcripts?

We prepared un-stranded RNA-Seq library (SMART-Seq2) and sequenced in Illumina platform. We mapped with STAR (by adding XS tag) and assembled using cufflinks RABT assembly. Now after comparing...

11 December 2018 2,352 1 View

Can anyone give me an ideas to build a database with functionality?

Currently I am designing a gene expression database in MySQL. Additionally I want give an web interface to the database, which is primarily for our lab use. And also I want to include some...

05 June 2018 6,305 2 View

What are the essential SNP filtering criteria one should follow before performing GWAS analysis?

We are working on a project where we need to perform genome wide association studies for multi-parental population. We have the SNP data from whole genome re-sequencing protocol. As I am quite...

09 October 2017 448 9 View

What are the considerations for choosing a statistical model to perform association studies?

07 August 2017 4,004 5 View

How to analyze BCFTools RoH output? How to provide information of in-house alternate allele frequency?

10 November 2016 571 1 View

Can anybody help me in understanding one variant reported in 1000Genomes phase three release?

11 December 2014 3,740 5 View

What if anyone removes all the unknown (or confusing) contigs from the reference genome (eg hg19) before alignment and other consecutive tasks?

There are a good number of contigs in the hg19 release. The coordinates of this contigs are a bit confusing. Now if anybody want to keep these contigs out of reference before doing alignment, what...

01 February 2014 7,190 3 View

Which variant caller researchers are using frequently?

I am developing/refining a pipeline for exome data. According to reported articles there are mainly two callers I found out to be more acceptable among researchers: One is SAMTools' variant caller...

10 November 2013 782 5 View

Is there any repositories where I can find a vcf file for dbSNP release 131?

I am looking for a vcf file of dbSNP release 131. Can anyone provide me with a link holding the data? Or is it possible to convert dbSNP flat files to vcf format by using any tool?

10 November 2013 7,781 7 View

How to correct SAM file for the errors reported by PICARD ValidateSAMFile ?

I am trying to validate SAM file for further downstream processing using picard ValidateSAMFile command. But getting four types of error for ~50000 reads. Summary coming as: Error Type...

09 October 2013 5,409 4 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