I need help in bioinformatics.. Can anyone assist me?

More Deblina Misra's questions See All

Is there any matlab code available for 28 test functions at CEC'13 Special Session on Real-Parameter Optimization?

I am currently working on PSO where i need to test my algorithm with benchmark optimization test functions. Liang et al publish this paper ( Problem Definitions and Evaluation Criteria for the CEC...

29 July 2020 5,123 2 View

Why does the transmission spectra shows an increase near the optical absorption edge?

Measuring a transmission spectrum of thin film (eg: single phase oxide) using UV-Vis spectroscopy, the transmission value gradually increases as we decrease the wavelength and reaches a peak until...

30 April 2020 700 1 View

Do you have GC-MS datasets that are not analyzed/ published yet?

Hello, I am looking for unanalyzed and unpublished GC-MS datasets from diverse mass spectrometer vendors ? Such as ToFs, single/ triple Quads, Orbitraps etc. that have been acquired from human,...

10 April 2020 2,347 10 View

Which fluorescent markers I can use to stain live dead cells treated with doxorubicin?

Hi, Which is the best live, dead flourescent stain to use if I have to image a spheroid treated with Doxorubicin. The standard live /dead assay kit has Calcien-AM (live) and ethidium bromide...

22 May 2019 7,668 1 View

What is the best tool to identify and provide a good pictorial representation of homologous DNA sequences between species?

I want to identify homologous DNA sequences between mouse chicken, xenopus and zebrafish for a human non coding genomic regions. Any suggestion of which tool to use. I would prefer the one that...

03 April 2018 2,394 3 View

Why do metal-oxide composites show higher permittivity/refractive index as compared to pure oxide?

Since metals (eg: Au) show negative permittivity, the metal oxide composite should should show lower permittivity compared to the pure oxide phase. But standard methods such as Effective Medium...

19 February 2018 6,009 1 View

What could be the probable reason of getting a ring during biofilm formation in unicoluted media?

I have been trying to optimize the biofilm formation for enterobacter cloacae for which the biofilm formation is sparsely studied. i have been facing great difficulty in the C.V assy. I am...

11 February 2018 3,910 6 View

High GAPDH values in qPCR

I use GAPDH as reference gene in qPCR runs. For one of my samples, I am repeatedly getting high Ct values of GAPDH (27-33). it's 20 or less for all other samples and control. I tried using its...

06 July 2017 7,543 5 View

How to avoid the cloudy appearance of media?

Since last few weeks, I'm facing a problem with my resistant 231 cell line. After every third or fourth passage, the media turns a little turbid in 2-3 days, and I have to thaw a fresh vial. But...

25 May 2017 3,853 4 View

Which seems to be a better option: using Plasma or Serum, for determining blood based protein biomarkers using MALDI-TOF & 2D?

In a study, we need to determine blood based protein biomarkers in stroke using proteomics techniques like MALDI-TOF-MS and 2D gel electrophoresis. So, which component of the blood should we use...

15 November 2016 304 3 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

How do I choose contrasts in SPM8?

I am learning how to use SPM for PET and PET-MR analysis, but I haven't found any great resources that explain how contrasts work. I have a series of PET images where our hypothesis argues that...

24 February 2021 1,534 2 View

Are there methods for automatically mapping floodplains, fans and terraces?

I want to map these river geoforms with as little subjectivity as possible. I have a high resolution DEM generated by drone data.

22 February 2021 7,800 3 View

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases...

22 February 2021 4,374 3 View

How to use Remote sensing and GIS applications for mapping the available medicinal plants within the locality/municipality?

Hello, I'm very interested in mapping and managing the conservation of the Philippine traditional medicinal plants, in which I think is very helpful in the field of medicine for further analysis...

21 February 2021 374 5 View

Plasmid amplification in S2 cell?

When co-transfect S2 cell with selection vector (pCoHygro or pCoBlast ) to make a stable cell line, does the gene integrate into the genome or just like E.coli? How do the plasmids amplify within...

09 February 2021 5,423 1 View

Useful architecture for bioinformatics?

Hi Dear researchers In ensemble-based architectural design Which algorithms are more useful for classification? What is the difference between parallel and ensemble architecture? Thanks I am...

08 February 2021 2,727 5 View

What are the limits of determining metastability in the brain?

What are temporal limits in determining brain metastability? In other words, how long does the minimum length of the scan segment using fMRI have to be for the result to be of any value? I'm...

07 February 2021 2,380 2 View

Electron density difference maps(Fo-Fc): what is the meaning of negative densities (red blobs)?

Dear community, As far as I understand, negative density features point at stuff that is in the model, but not supported by experimental data. However, in many cases (e.g. attached image), when...

06 February 2021 2,847 2 View

Are the hyperspectral image datasets which are publicly available at ehu.eus website atmospherically and geometrically correct?

I've come across a couple of publicly available hyperspectral image datasets from the website http://www.ehu.eus/ccwintco/index.php/Hyperspectral_Remote_Sensing_Scenes Now, my concern is...

05 February 2021 3,550 1 View

Abhijeet Singh

What do you need help in?

Matthew Edward Thornton

Hello! There are a number of ways to proceed. A very popular software for doing alignments to reference genomes is STAR. STAR also has a very nice manual with all of the information you need to perform alignments. https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf If you want to do other things, I would look at the bioconductor website first. Then I would look at the Salk institute's HOMER software and especially their tutorials. Good luck!!

Feng Yan

If you are talking about aligners. You have two categories of choice.

Splice-aware for RNA-seq etc, such as STAR, hisat2.

Splice-unaware for ChIP-seq, WGS, such as bwa, bowtie2.

Deblina Misra

@abhijeet Singh I want to map my a targeted gene of a specific cell line model to that of the species. The cell line genome has been sequenced and all the gene sequences of the species. which bio informatics tool or technique can be used to study so?

Pattarasiri Rangsrikitphoti

TopHat2 is a nice aligner that also considers splice junction. And if you want to do further steps like differential gene expression this tool will work perfectly in the tuxedo suite package (Cufflinks,...)