User: umeshtanwar2

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umeshtanwar210
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Posts by umeshtanwar2

<prev • 34 results • page 2 of 4 • next >
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Comment: C: Running GSEA for DEGs
... Thank you for the response. These are the official gene symbols for Arabidopsis. ...
written 10 months ago by umeshtanwar210
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Running GSEA for DEGs
... Hi all, I am working on RNA-seq data of Arabidopsis plant. I have a list of Deferentially Expressed Genes obtained from DESeq2. Now I would like to do further analysis using GSEA. I prepared the rank file by using the code below: x <- read.csv("DEG-B_vs_A.csv") attach(x) x$fcSign=si ...
next-gen rna-seq written 10 months ago by umeshtanwar210 • updated 10 months ago by Prakash1.8k
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Comment: C: DESeq2: Differential gene expression
... Thank you so much @swbarnes2. I am more clear about interaction effects after reading this tutorial. ...
written 10 months ago by umeshtanwar210
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Comment: C: DESeq2: Differential gene expression
... Thank you a lot @i.sudbery. This was really very helpful. ...
written 10 months ago by umeshtanwar210
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Comment: C: DESeq2: Differential gene expression
... Thank you so much @ i.sudbery. ...
written 10 months ago by umeshtanwar210
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DESeq2: Differential gene expression
... Hi, I am working on RNA-Seq data for Arabidopsis plant. I have samples from 4 genotypes (A, B, C, D), Untreated and after treatment, with 3 replicates for each. I used STAR for alignment and obtained count.txt file by using featureCounts. Now I am doing the DGE analysis by DESeq2. My coldata looks l ...
R rna-seq written 10 months ago by umeshtanwar210 • updated 10 months ago by swbarnes27.4k
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(Closed) DESeq2: Differential gene expression
... Hi all I am working on the RNAseq data of Arabidopsis thaliana. I have done the differential gene expression analysis by using DESeq2. Now I have a list of DE genes (gene ID) in csv file. How can I have the names and description of the genes in my DE genes results file? My file looks like this: ...
rna-seq written 11 months ago by umeshtanwar210
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Comment: C: Differential gene expression DESeq2
... 1 araport11 exon 3631 3913 . + . transcript_id "transcript:AT1G01010.1"; gene_id "gene:AT1G01010"; gene_name "NAC001"; Name "AT1G01010.1.exon1"; constitutive "1"; ensembl_end_phase "1"; ensembl_phase "-1"; rank "1"; biotype "protein_coding"; transcript_id "AT1G01010.1"; protein_id "AT1G01010.1"; ...
written 11 months ago by umeshtanwar210
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Comment: C: Differential gene expression DESeq2
... I am facing this problem: //================================= Running ==================================\\ || || || Load annotation file oldArabidopsis_thaliana.TAIR10.42.gtf ... || Warning: failed to find the g ...
written 11 months ago by umeshtanwar210
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Comment: C: Differential gene expression DESeq2
... Thank you so much @Kevin. I will do this when using featureCounts. ...
written 11 months ago by umeshtanwar210

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