User: amy16

gravatar for amy16
amy1610
Reputation:
10
Status:
New User
Location:
Last seen:
1 day, 6 hours ago
Joined:
4 months, 1 week ago
Email:
a**************@gmail.com

Posts by amy16

<prev • 68 results • page 1 of 7 • next >
0
votes
1
answer
72
views
1
answer
Tools to do a linear or logistic regression of DEG
... Hi all, I have completed the DEG analysis following the new tuxedo pipeline and have ended up with a long list of genes/transcripts. I was thinking of doing a linear or logistic regression analysis on this list to get the best pick of the gene/ transcript that could be associated with the molecular ...
rna-seq deg written 1 day ago by amy1610 • updated 1 day ago by Kritika170
0
votes
0
answers
51
views
0
answers
RNA-seq read alignment to ref. genome-mismatch penalty
... Hi all, What is the advised the --mp MX,MN values to capture most of the splice variants present in the given transcriptome? Thanks Amritha ...
rna-seq hisat2 written 3 days ago by amy1610
0
votes
1
answer
71
views
1
answers
Comment: C: Phenotype data analysis for QTL validation
... Thanks for your reply. ...
written 4 days ago by amy1610
0
votes
1
answer
71
views
1
answer
Phenotype data analysis for QTL validation
... Hi all, While validating a QTL interval markers in a different set of genotypes (300 lines) from the RIL mapping population that had been originally used for the QTL identification study, do I have to use the same model that was used for the analysis while identifying the QTL interval? PS: The pheno ...
genetics qtlmapping validation written 5 days ago by amy1610 • updated 5 days ago by theobroma221.1k
0
votes
0
answers
113
views
0
answers
Understanding the gffcompare output for my dataset
... Hi all, Below is the output from gffcompare of assembled transcripts from my RNA-seq experiment with the reference genome annotation. I am concerned about the low precision values. Do I have to rerun my assembly? # Query mRNAs : 74136 in 32930 loci (63219 multi-exon transcripts) # ...
tuxedo rna-seq gffcomapre written 4 weeks ago by amy1610
0
votes
1
answer
125
views
1
answers
Comment: C: Estimating the abundance of the transcripts and genes using stringtie
... Thanks for your valuable suggestion. Very helpful for a beginner like me in this aspect to improve my understanding. ...
written 5 weeks ago by amy1610
1
vote
1
answer
125
views
1
answer
Estimating the abundance of the transcripts and genes using stringtie
... Hi, Given that the genes and isoforms present in one sample are rarely identical to those present in all other samples in a given experiment, and so they need to be assembled in a consistent manner so that they can be compared, so we merge these GTF files into one single file. When merging is it adv ...
stringtie rna-seq written 5 weeks ago by amy1610 • updated 5 weeks ago by Devon Ryan76k
0
votes
0
answers
159
views
0
answers
Comment: C: Clarification in the workflow steps of the RNA-seq analysis for differential gen
... Thanks for directing me!!!! ...
written 5 weeks ago by amy1610
0
votes
0
answers
159
views
0
answers
Clarification in the workflow steps of the RNA-seq analysis for differential gene analysis
... Hi all, I am using Stringtie for transcript assembly and quantification. My experimental design includes 4 different genotypes each under two treatment conditions with sim to identify differential gene expression analysis. I did the sequence alignment to the reference genome and the used Stringtie ...
assembly stringtie tuxedo rna-seq written 5 weeks ago by amy1610
0
votes
0
answers
126
views
0
answers
specification of linear model and log transformation in ballgown
... Hi, I am following the 'new tuxedo' protocol for my RNA-seq data analysis for Differential gene expression analysis. My experimental design includes 4 varieties, each with control and treatment. I aim to study the varietal effects and the treatment effect. Does the stattest function which includes ...
package function R ballgown rna-seq written 5 weeks ago by amy1610

Latest awards to amy16

Rising Star 6 weeks ago, created 50 posts within first three months of joining.
Scholar 3 months ago, created an answer that has been accepted. For A: RNA-seq read alignment

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 669 users visited in the last hour