22 Questions 46 Answers 0 Followers
Questions related from Snijesh V.P.
which platform is better for performing microarray data analysis? agilent, affymetrix or illumina
10 April 2021 3,846 3 View
Tumor mutational burden (TMB) is a measure of the number of gene mutations inside the cancer cells. TMB of a tumor sample is calculated by the number of non-synonymous somatic mutations per...
02 September 2020 4,653 1 View
Is there any database or tool where I can retrieve list of proteins detectable by immune histochemistry (IHC)?
03 August 2020 7,651 2 View
what is the longest deletion or insertion that can be detected in next generation sequencing data analysis
27 February 2020 2,938 3 View
I have analyzed the dataset of GSE38132 from gene expression omnibus. The data is from cell line breast cancer ZR-75-1 which comprises of 9 conditions with 4 replicates for each condition making...
17 February 2020 5,906 4 View
I have 4 sample [control, pre-treatment, post-treatment, metastais] with 4 replicates which make total 4x4 = 16 samples I want to perform comparison of control with all other groups. For the said...
13 February 2020 6,358 2 View
I have two batches of samples which were collected during two time period. If I perform batch correction to remove batch effect will it affect the downstream analysis of gene expression studies?
20 December 2019 864 3 View
I want to extract the data from the internet with specific medical terms. Which are the available tools with best accuracy or output?
07 February 2018 6,729 5 View
Hi, I think there are about 80 organs in the human body. When I searched for list of all organs different sites are showing different list. Are there any books or publication that clearly mentions...
11 November 2017 8,855 4 View
I want to detect the somatic mutations for breast cancer disease. Can anyone tell me about the major differences in detecting somatic mutations from blood sample and tissue samples
21 July 2017 10,066 3 View
May be a general question; sometimes stupidity too.... For example, cancer is caused by somatic mutation in the genome. And treatment has been given to the patient. So what is the chance of change...
18 July 2017 7,692 4 View
I know it is possible to identify germline mutations from the blood sample. But, I have serious doubt regarding detecting somatic mutations from the blood sample. Generally, somatic mutations are...
12 July 2017 8,010 9 View
Which all tools or packages would you recommend to me for clinical NGS data analysis. The aim is, at the end, I need the output with the best accuracy Tools or packages which I have...
07 July 2017 7,529 7 View
Presently, there are many methods to calculate functional similarity (semantic similarity) between the genes. But there are three domains associated with any gene i.e., Molecular Function (MF),...
17 May 2017 4,163 2 View
I want to perform most accurate variant calling by implementing a perfect pipeline. I want to predict both somatic and germline mutations Please tell me your suggestions.
14 March 2017 418 11 View
I want to align my reads to reference genome. To date several tools are avilable like BWA, bowtie2 etc. Which tool is more accurate, sensitive and rapid for the said purpose? Thanks
06 March 2017 1,041 7 View
I am expecting most reliable and frequently mutated genes for Breast Cancer in Indian Population. Is text mining the only option?
02 March 2017 5,133 1 View
My plan is to develop a tool that predicts mutations in user input genome. I have collected some set of genes and their corresponding sequence. The nucleotide sequence positions of genes are...
13 February 2017 9,073 2 View
In genome data, gene is specified as TP53 with chromosome location (chr17:7565097-7590856). But when I serached this region in NCBI-Nucleotide,...
06 February 2017 5,443 4 View
I have set of genes with their nucleotide sequence (includes exons, introns everything) and I want to extract only coding region from these sequence. 1. How can I do it? 2. Is there any online...
04 February 2017 6,010 3 View
Recently, I came to know about a mobile DNA sequencer launched by Oxford (MinION). 1. What about Its efficiency and the reagents required for sequencing? 2. What are data anlysis tools used, once...
30 January 2017 880 2 View
Using FastQC, I have checked the over all quality of the file. The output file contains much count of over represented sequences. I simply performed blast on these sequences, and surprisingly they...
29 December 2016 4,266 6 View
