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• How Should I Include Biological Replicates In Cufflink/Cuffdiff?
  Dear team, I have a few questions regarding RNA-seq data analysis. I want to compare transcripto...
• Cuffmerge Question
  I'm new to RNA-Seq analysis and think this question must have been asked before, but I can't find...
• Multiple FASTQ files per replicate
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• Cuffdiff-differential gene expression-NOTEST
  Hi I am just starting up and getting to know and analyze my data from the RNA-seq. I have 2 biol...
• Rna-Seq Cds, Splicing And Tss Fails
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• Rna-Seq Analysis
  Since the pictures are too big for the mailling list. I will upload it in seperate emails. Dear ...
• RNA seq beginner
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• Rna-Seq Analysis
  Dear all, I am using Galaxy for RNA-Seq analysis. I expect two lists: differentially expressed tr...
• Analyzing Rna-Seq Replicates Using Cuff(Links/Compare/Diff)
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• RNA-seq pipeline standard?
  I'm not following the new trends specifically for rna-seq so are there something more innovative ...
• what is a "Tabular file with Transcript - Gene mapping" in DESeq2?
  I have RNA Seq data from two conditions using a non-model organism. I constructed a trinity assem...
• 100 GB bam dataset fails conversion to bam.bai
  Hi! I'm a beginner to RNA-Seq world and need assistance to correctly analyze our dataset. I'm wo...
• Finding exogenous transcripts in RNA-Seq bam files
  Hello, What is the easiest way to find and count reads for exogenous transcripts (Cre, GFP, etc....
• Extract Spliced Transcripts From Cuffmerge
  Hi All, I have mapped RNA-Seq reads to an unannotated partial genome assembly and assembled them...
• Phenotype data for Ballgown tool
  Hello I am doing RNA-seq analysis using local server galaxy. I'm following the new Tuxedo protoco...
• Using different reference genome yields different results in RNA-seq data analysis
  Hello, I've got some questions with my RNA-seq results generated by galaxy.  For the experiment,...
• 'Sampling' Bam or BigWig files?
  I am involved in an RNAseq project in which mutliple tissues of an organism are being analysed. N...
• Are reads number normalized on transcript length ?
  Hello, I used featurecounts to obtain reads number from a RNA-seq file (.bam). I would know if t...