30 Questions 76 Answers 0 Followers
Questions related from Snijesh V.P.
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...
02 February 2020 5,270 2 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...
02 February 2020 8,636 4 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?
12 December 2019 1,405 3 View
dbSNP has got different build (140 to 151). Does the latest version dbSNP build 151 have all snp ids (rsids) that are present in previous build
07 July 2018 4,741 0 View
Some database like ebi gwas provides odds ratio for snps. I wanted to know whether clinvar database provides the same?. I have whole data of clinvar in excel but I can not find odds ratio in it.
06 June 2018 9,725 2 View
I want to extract the data from the internet with specific medical terms. Which are the available tools with best accuracy or output?
02 February 2018 9,883 7 View
Consider, 4 research paper with different methodologies to prioritize genes. Combining these methods to single pipeline, can we call it as a "novel method" as together they can not be found in any...
02 February 2018 10,109 2 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 1,083 5 View
What is the present status of Next Generation sequencing in Clinical Diagnosis?. Is it well defined to make a conclusion for diagnosis?.
11 November 2017 8,905 3 View
RNA-Seq is well known for calculating transcript expression. But, researches also do variant calling on RNA-seq data. In such case all mutations can't be identified due to alternative splicing....
08 August 2017 8,228 8 View
I have seen some tools which converts SAM to BAM format. I wanted to know how they are converted. SAM file contains nucleotides (A, T, G, C) and how these data are converted to binaries?
08 August 2017 4,282 4 View
I performed RNA-Seq data analysis using protocol given in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/. When I am using cummerbund package, it shows output like this: CuffSet instance...
08 August 2017 7,231 3 View
Suppose I have a fastq sample file with adaptor content in it. I believe adaptors in the sequence will not get mapped to the reference genome. If you have contrasting answers what is the chance of...
07 July 2017 10,001 21 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 6,382 12 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...
07 July 2017 9,675 10 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
07 July 2017 3,073 4 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),...
05 May 2017 1,120 1 View
05 May 2017 9,927 2 View
I have reference genome as hg19.fa and duplicate removed reads using picard as deduped_reads.bam. Next, I am trying to run the command java -jar...
03 March 2017 933 1 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
03 March 2017 7,347 7 View
I have downloaded a sample from http://www.ebi.ac.uk/ena/data/view/PRJEB19339 (ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR181/004/ERR1817984/ERR1817984.fastq.gz) and I have checked the quality of the...
03 March 2017 1,042 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.
03 March 2017 1,004 12 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...
02 February 2017 6,800 2 View
I want to know more about this online portal. 1. What all service they provide? 2. What all we can carry out on this portal
02 February 2017 9,813 1 View
I have perfromed NGS analysis (data is paired end) and in the output genes with genome location is given. I want to know whether the location is given from 3'-5' region or 5'-3' region? For...
02 February 2017 4,114 4 View
Mitochondrial DNA are located outside nucleus wheras genomic DNAs are inside nuclues. So is it possible to sequence both type of DNA at a run
01 January 2017 2,530 2 View
I am trying for a comparative breast cancer study across all population focusing on mutations in gene. So, in disease like cancer, mainly what type of mutations are focussed? Multiple mutation...
01 January 2017 3,831 1 View
While using cladist.jar, I get following message: "Out of memory, allocate more RAM, try command line: -Xmx###M to increase the maximum amount of memory in megabytes that the JVm is to use"
03 March 2014 8,214 1 View
.
09 September 2013 3,769 6 View
Rheumatoid Arthritis
09 September 2013 3,945 1 View
