User: amy16

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amy1640
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Posts by amy16

<prev • 72 results • page 1 of 8 • next >
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(Closed) Ballgown's statistical test
... Hi, Can Ballgown statistical test be used to do differential expression analysis for control vs treatment groups each including 3 replicates? -Thanks ...
rna-seq diffferential expression analysis written 10 months ago by amy1640
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Recommended sequencing coverage for WGRS
... Hi all, What is the recommended sequencing coverage for whole genome resequencing data for SNP identification? Thanks ...
next-gen sequencing written 18 months ago by amy1640 • updated 11 months ago by Biostar ♦♦ 20
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minimum recommended length for transcript prediction -Stringtie
... Hi all, Can you please advise me on what is the minimum recommended length for transcript prediction? I am using PE reads and Stringtie tool to run the transcript assembly. Thanks ...
stringtie pe rna-seq written 18 months ago by amy1640
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Comment: C: Tools to do a linear or logistic regression of DEG
... Which package in R do you recommend that will be more suitable for this type of analysis? ...
written 18 months ago by amy1640
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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 19 months ago by amy1640 • updated 19 months ago by Kritika260
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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 19 months ago by amy1640
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Comment: C: Phenotype data analysis for QTL validation
... Thanks for your reply. ...
written 19 months ago by amy1640
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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 19 months ago by amy1640 • updated 19 months ago by theobroma221.1k
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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 20 months ago by amy1640
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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 20 months ago by amy1640

Latest awards to amy16

Popular Question 18 months ago, created a question with more than 1,000 views. For SAMtools installation on windows
Rising Star 20 months ago, created 50 posts within first three months of joining.
Scholar 22 months ago, created an answer that has been accepted. For A: RNA-seq read alignment

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