Jayesh kumar Sundaram

10 Questions 11 Answers 0 Followers

Questions related from Jayesh kumar Sundaram

How to identify marker genes from Single Cell RNA seq data?

I am currently working with scRNA-seq data. I have to rank or score genes based on how spatially expressed they are. Is there any good measure or tool to do that?

24 August 2020 4,097 3 View

Why do the reads from the regular non-strand specific RNA-seq experiment predominantly map to either + or - strand but not 50%, for a particular gene?

I have sequencing reads from non-strand specific RNA-seq experiment. When I look at read alignments for individual genes, the reads predominantly map to either positive or negative strand. Why is...

30 April 2020 8,921 0 View

How to reproduce eigengenes calculated using WGCNA package?

I identified eigengenes for all gene modules using WGCNA. I am trying to reproduce the eigengenes using prcomp function to get the PC1. PC1 and eigengene values are not matching. What am I missing?

25 March 2020 1,465 2 View

Fastq file has number code rather than nucleotide in the sequence, Why?

What's wrong with the following fastq file? Why don't I see any nucleotides? @SRR867022.1 s0205_20091123_4_Boot2_1_2_22_F3...

17 February 2020 8,041 5 View

How to perform Pearson correlation coefficient calculations on RNA seq fold change values?

I have gene expression data from different conditions from different studies. Instead of using the actual TPM values for Pearson Correlation coefficient (PCC) calculation, I have decided to use...

19 December 2019 6,477 1 View

Have you used any database for interaction data collection? Can you help me with Arabidopsis Interaction viewer database, university of toronto?

I am getting interaction data from Arabidopsis interaction viewer database, maintained by toronto. I am trying to separate out protein-protein interaction and protein-DNA interaction. The data...

04 November 2017 6,359 1 View

How to get the promoter sequence of a gene? I want to get it from RSAT Plants. Do I have to get the upstream sequence form a gene or mRNA?

I want to get the promoter sequence of some genes. Should I get it from upstream of the gene or mRNA? How is gene defined in RSAT plants?

24 August 2017 6,083 4 View

How to analyze expression levels of genes across datasets in microarray?

I am working on some of the microarray data of some of the genes I am intersted in. I wanted to know the expression levels of some of the genes in different cell types. People have deposited data...

06 July 2017 8,065 5 View

What is given in gene expression csv file from BDGP?

In the file all the column has gene expression data. I couldn't understand what those values are.

04 December 2016 7,423 3 View

Can anyone suggest a nice nuclear localised antibody for epithelial cells in drosophila?

i strictly want a nuclear localised antibody. thank you.

02 November 2015 1,755 10 View