Can anyone suggest a tool to detect contamination in NCBI Illumina high-seq transcriptome databases?

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Does anyone have any idea why Polynucleotide kinase (PNK) phosphorylation of primers may fail?

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What is the best way of analyzing spatial and temporal variation in species composition and abundance dataset?

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fatal error

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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 ??:?

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Srinivas M Srikanth

Hi Bilgenur,

Do you mean vector sequences?, you can use the NCBI Univec database sequences and match with the RNA-Seq data to eliminate any contaminating sequences. Follow this link for more information:

https://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/

Deepika Srivastava

VECSCREEN only screens the vector sequences not removes them so you have to write a script to remove it (I used it personally). You can use SeqClean tool it will remove all the vectors then input its .cln and .qual file into "cln2qual". I think it will work for you. :)