User: umeshtanwar2

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umeshtanwar210
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Posts by umeshtanwar2

<prev • 29 results • page 2 of 3 • next >
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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 19 days ago by umeshtanwar210 • updated 19 days ago by swbarnes25.3k
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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 6 weeks 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 6 weeks 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 6 weeks 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 6 weeks ago by umeshtanwar210
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Comment: C: Differential gene expression DESeq2
... I obtained the gff3 file from: [Arabidopsis release 42][1] Please suggest me if it is correct to convert the gff3 to gtf for featureCounts? [1]: http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index ...
written 6 weeks ago by umeshtanwar210
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Comment: C: Differential gene expression DESeq2
... Thank you Kevin. I used the STAR for alignment of reads on reference with using annotations in gff3 file format. Then I used featureCounts for prior to DESeq2. I converted annotation file gff3 to gtf for using in featureCounts. Did it make the difference? ...
written 6 weeks ago by umeshtanwar210
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Differential gene expression DESeq2
... 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 of the genes in this file? My file looks like this: baseMean log2FoldChange lfcSE ...
rna-seq written 6 weeks ago by umeshtanwar210
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Comment: C: Differential gene expression by DESeq2
... Thank you @i.sudberry. It was really helpful for me. ...
written 7 weeks ago by umeshtanwar210
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Comment: C: Differential gene expression by DESeq2
... Thank you @i.sudbery. It worked. Its showing: out of 25686 with nonzero total read count adjusted p-value < 0.05 LFC > 1.00 (up) : 627, 2.4% LFC < -1.00 (down) : 2473, 9.6% outliers [1] : 0, 0% low counts [2] : 2944, 11% (mean count < 1) [1] see 'cooksCutoff' argument of ? ...
written 8 weeks ago by umeshtanwar210

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