How can we correct pacbio long-reads with Illumina data?

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How can you bring two structures together to create an adhesive bond in LAMMPS?

I have created an Ice 1h crystalline structure and an Aluminium substrate structure and equilibrated both at 250K. Now I need to bring them together in a way that an adhesive bond is created....

01 March 2021 3,325 2 View

FDC and FRC cell populations in mouse spleen?

I was trying to isolate fibroblastic reticular cells (FRC) and follicular dendritic cells from mice spleen, but kept getting poor yield. I found from literature that the frequency of FDC is around...

17 February 2021 3,506 4 View

How to raise temperature in small increments during equilibration in LAMMPS?

All, I am trying to equilibrate an Ice 1h crystalline structure to 250K in LAMMPS. When I tried to do this at 250K directly, the structure lost it's crystalline shape and became disordered post...

14 February 2021 5,747 2 View

Can anyone please suggest where I can find a reference for ReaxFF parameters for PTFE(Teflon) suitable for use in LAMMPS?

Trying to simulate a ice-PTFE interaction and am unable to find a reference which actually lists out forcefield parameters for PTFE-PTFE interactions using ReaxFF or even other force fields like...

08 February 2021 9,373 2 View

Are the topics below viable research in plant biotechnology?

1. Chemically induced mutagenesis in seed and qPCR detection and amplification of desired trait. 2. Site-directed mutagenesis in qualitative traits of a multiline seed.

04 February 2021 9,069 3 View

Should the Ice 1h crystalline structure be lost during equilibration process in LAMMPS?

I have created an Ice 1h structure and am equilibrating it 100K in NVT ensemble in LAMMPS for a timestep of 0.25fs in 3000 steps. The potential used is TIP4P/Ice. Although the simulation runs fine...

26 January 2021 9,603 11 View

Fluorophore panel selection?

Hello, I'm trying to select fluorophores for a large panel of flow cytometry, so I'm wondering what is the maximum degree of overlap between two fluorophores that is considered acceptable? Thanks.

19 January 2021 3,475 3 View

Running a Kruskal-Wallis test on a large sample with a likert scale on excel?

Hi everyone, I would like to run a Kruskal-Wallis test on a large sample with a likert scale. I am having difficulties figuring out how to process with the ''rank_avg'', and rank sum with such a...

05 December 2020 793 3 View

What is the relationship between pressure vacuum and pore water emptying?

Hello everyone, When I put a wet sample in a vacuum desiccator, the larger pores tend to empty. I would like to know if there is a relationship between vacuum pressure and the size of emptied...

25 November 2020 9,967 5 View

Any explaination for change signs and significant level of control variables in regression?

I have 2 sets of regression estimations with same dependent variables, same control variables and model. In the second regression, there are two additional variables. However, the sign and...

28 September 2020 6,304 6 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

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

27 February 2021 547 3 View

I want to performe MALDI-TOF MS for bacterial identification, I would appreciate it if anyone can tell me the matrix solution preparation protocol ?

based on what I've studied on multiple papers, for peptide and protein identification Alpha-cyano-4-hydroxycinnamic acid (CHCA) is an appropriate matrix to use, I also know that the CHCA powder...

26 February 2021 6,799 3 View

Has anyone used the Illumina ITS1 primer sets?

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25 February 2021 6,969 3 View

Errors in DNA sequences?

I am trying to better understand the scope of DNA replication and sequencing errors, e.g. 1. I have seen similar error rates of 10e4 to 10e5 for cell & instrumental DNA replication,...

24 February 2021 4,397 3 View

Universal bacterial primers targeting a mRNA?

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22 February 2021 9,969 3 View

Can I use FLEXBAR to detect and remove barcodes out of my short reads without demultiplexing ?

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22 February 2021 9,873 3 View

Does anyone have any ideas why drug-resistant malaria is increasing in Southeast Asia even when those drugs are no longer used?

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21 February 2021 6,084 5 View

I can detect my protein but the encoding DNA sequence has stop codons within. Should I ignore the stop codons?

I constructed a synthetic DNA library (scFv, VH-VL orientation) with a 3' reporter and 8x histag. I cloned and expressed this gene following which I performed an ELISA. The ELISA results suggested...

19 February 2021 7,006 5 View

Eric Antoniou

HI Vincent

You may want to contact Michael Schatz at Cold Spring Harbor ([email protected]). Mike is a co-author of the first error correction method and he has a lot of experience with PacBio only and hybrid illumina/pacbio de novo assemblies

Eric

Jaime Jiménez-Ruiz

Hi Vicent,

do you finally find the tool to correct PacBio using Illumina data? it would be interesting if you share this info.

I found LoRDEC tool to do this, (an accurate and efficient long read error correction-http://bioinformatics.oxfordjournals.org/content/early/2014/08/27/bioinformatics.btu538.abstract), but I am interested if there are more programs like this.

Jaime