User: rthapa
rthapa • 0
- Reputation:
- 0
- Status:
- New User
- Last seen:
- 16 hours ago
- Joined:
- 1 year, 2 months ago
- Email:
- r*****@tamu.edu
Profile information, website and location are not shown for new users.
This helps us discourage the inappropriate use of our site.
Posts by rthapa
<prev
• 18 results •
page 1 of 2 •
next >
0
votes
1
answer
224
views
1
answers
... 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
rthapa • 0
• updated
2 days ago by
Kevin Blighe ♦ 39k
0
votes
0
answers
1.2k
views
0
answers
... 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
rthapa • 0
0
votes
1
answer
224
views
1
answers
... 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
rthapa • 0
0
votes
1
answer
70
views
1
answer
... 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 ...
written 3 days ago by
rthapa • 0
• updated
2 days ago by
Kevin Blighe ♦ 39k
0
votes
2
answers
667
views
2
answers
... 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
rthapa • 0
0
votes
1
answer
88
views
1
answer
... 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 ...
written 10 days ago by
rthapa • 0
• updated
7 days ago by
Kevin Blighe ♦ 39k
0
votes
1
answer
143
views
1
answers
... 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
rthapa • 0
1
vote
1
answer
143
views
1
answer
... 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 ...
written 13 days ago by
rthapa • 0
0
votes
1
answer
106
views
1
answer
... 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 ...
0
votes
1
answer
201
views
1
answers
... 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
rthapa • 0
Latest awards to rthapa
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 863 users visited in the last hour