User: BIOTECH.DEEPTI911

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Posts by BIOTECH.DEEPTI911

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overrepresentation enrichment analysis WebGestalt
... Hi Folks, I have done overrepresentation enrichment analysis (ORA) using online tool WebGestalt. In this analysis I only got the enrichment in the cellular component category and not in the other two (biological process and molecular function). I have also done this analysis by using other means ...
rna-seq written 4 months ago by BIOTECH.DEEPTI9110
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Comment: A: Small RNA-seq experimental design, pooling samples or not ? which one is better?
... Hey Folks, I also need some help in this regard. I am having RNA-seq data of pooled samples from cell line i.e. Control, Treatment 1 and Treatment 2 all with pooled RNA of triplicates to get 3 samples (1 for control, 1 for treatment 1, 1 for treatment 2). What strategy I should follow to get the max ...
written 4 months ago by BIOTECH.DEEPTI9110
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Answer: A: PANTHER vs WebGestalt
... Hi Sanathoi, I am also dealing with the same NGS data. You can use BinGO, a cytoscape plugin which is very useful as you can visualize the data. WenGestalt is more easy to use. ...
written 4 months ago by BIOTECH.DEEPTI9110
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Answer: A: Replicates for RNA-seq from 1 cell line undergoing different treatments
... Hi all, I am also doing the RNA-seq studies without replicates. I also got confused because I got the log2 fold change values but not the p-value. Is this fine to select the DEG's based on the fold change rather on the basis of p-value? Please shed some light on this. Dear Azyob as far as my know ...
written 4 months ago by BIOTECH.DEEPTI9110
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Comment: C: Problem in selecting threshold value for FPKM
... Yes Kevin exactly. As I do have the raw files with me I can do wonder with this data. A whole lot of information. I just need to get into its deeper insights and that's the reason I am keen to look at each and every single part of it :) ...
written 4 months ago by BIOTECH.DEEPTI9110
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Comment: A: Problem in selecting threshold value for FPKM
... Yes Kevin, I am just interested to find out the differentially expressed genes and major pathways involved for my treatment condition. Many authors have done the preliminary studies (that too with microarray) on that particular treatment but I am studying it in terms of global cellular outcomes by u ...
written 4 months ago by BIOTECH.DEEPTI9110
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Comment: C: Problem in selecting threshold value for FPKM
... Yes Kevin I do have the raw files i.e. Fasta files for my data, but I don't know how to analyse them:( Deepti Mittal Ph.D. Research Scholar C/O Dr. Gautam Kaul Division of Biochemistry NDRI, Karnal. ...
written 4 months ago by BIOTECH.DEEPTI9110
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Comment: C: Problem in selecting threshold value for FPKM
... Ok I should not use FPKM as this will be a bad decision. I will use the DEseq2 for differential gene expression for better analysis. Thank you so much to enlighten me. Your valuable suggestions helped me a lot :) ...
written 4 months ago by BIOTECH.DEEPTI9110
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Comment: A: Problem in selecting threshold value for FPKM
... Thank you Kevin for your comment. It is very helpful to increase my knowledge, but I want to know that what if I will take RPKM values instead of FPKM for DEG's analysis, would this approach be fine? Also I want to ask that I am using the topmost differentially expressed genes, is this approach is f ...
written 4 months ago by BIOTECH.DEEPTI9110
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Comment: C: Problem in selecting threshold value for FPKM
... Dear Vijay, Yes I completely agree that similar questions have been asked by others but the details they have provided is different form my question. I need the explanation for density plots so for this I have mentioned my work plan. It would be great if you will open this coversation. Regards, D ...
written 4 months ago by BIOTECH.DEEPTI9110

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