User: rthapa

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rthapa0
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Posts by rthapa

<prev • 18 results • page 1 of 2 • next >
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Comment: C: ANOVA or Linear regression for RNAseq data analysis with 3 factors
... Hi Kevin, Thanks you for the response. When I use results(), I get something like this; results(DESeq.A) log2 fold change (MLE): GenotypeDarij.Trttreatment LRT p-value: '~ Genotype + Trt + Genotype:Trt' vs '~ Genotype + Trt' DataFrame with 35225 rows and 6 columns I think the ou ...
written 2 days ago by rthapa0 • updated 2 days ago by Kevin Blighe39k
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Comment: C: Preforming differential expression (DE) on edgeR with control and different geno
... Hi Devon, I want to use two factorial model (two genotypes and two level of treatments) for analysis using DESEQ2. I want to see the interaction terms and main effects separately. I want to check if the gene expression is affected by treatment only or if the gene expression is effected by genotype ...
written 2 days ago by rthapa0
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Comment: C: ANOVA or Linear regression for RNAseq data analysis with 3 factors
... Hi Kevin, Can we check if the main effects or interaction effects are significant in DESEQ2? I want to see if the interaction effect is significant but I couldn't see the p-value of interaction and main effects separately in DESEQ2? I might be missing something. Do you have any insights on this? T ...
written 2 days ago by rthapa0
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Significance level of each variable used in the model
... Hi, I want to use two factorial model (two genotypes and two level of treatments) for analysis using DESEQ2. I want to see the interaction terms and main effects separately. I want to check if the gene expression is affected by treatment only or if the gene expression is effected by genotype only o ...
rna-seq written 3 days ago by rthapa0 • updated 2 days ago by Kevin Blighe39k
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Comment: C: What are the requirements to use data generated in other microarray experiments
... Hi Andrew, I have a similar case. I have a two factorial design (genotypes and treatment effects). My control samples are from Novaseq and treated samples from Hiseq. Is there a way to deal this situation? According to your previous comments, there is no way to deal the unbalanced design. Thanks ...
written 6 days ago by rthapa0
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Haplotypes analysis from SNP chip data
... Hi, I want to do Haplotypes analysis and comparison of different genotypes from SNP chip data. Do you have any suggestion on the tools that I can use for? Thanks ...
snp written 10 days ago by rthapa0 • updated 7 days ago by Kevin Blighe39k
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Comment: C: r2 and LD value estimation between significant SNPs identified from GWAS
... Thank you for your reply. Finally I could use TASSEL to get r2 value. I wanted to see LD decay using r2 and distance but my plot looks weird. Do you have any idea? Thanks! ...
written 10 days ago by rthapa0
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r2 and LD value estimation between significant SNPs identified from GWAS
... Hi, I want to estimate r2 value and LD value among the significant SNPs discovered from GWAS analysis. Could anyone suggest me what R package is the best and what file format is needed? I would appreciate it. Thanks ...
R snp written 13 days ago by rthapa0
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Comparison of samples of different read lengths in differential gene expression analysis
... Hi, I have a sequenced data of 75 bp PE for control samples and 150 bp PE for treatment samples. I am using HISAT2 for mapping and alignment. I got a gene count matrix after using Stringtie. I am wondering if I could use the gene count matrix directly for DESEQ2 for the differential gene expression ...
rna-seq written 5 weeks ago by rthapa0 • updated 5 weeks ago by swbarnes25.0k
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Comment: C: extra gene ids in gene count matrix than in gtf file
... For the stringtie, I used the following command; stringtie /scratch/user/rthapa/RNA-seq/rnaseqS10.hisat.sorted.bam -o /scratch/user/rthapa/RNA-seq/rnaseqS10.gtf -p 8 -G /scratch/user/rthapa/RNA-seq/Oryza_sativa.IRGSP-1.0.37.gtf -A /scratch/user/rthapa/RNA-seq/gene_abund -e And to convert the gtf fi ...
written 5 weeks ago by rthapa0

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