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• 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...
• DESeq2 gives fold changes for transcripts with zero counts in all samples
  I have run DESeq2 on transcript counts generated by String Tie. For some transcripts, I have zero...
• Annotation file formats .gff3 to .gtf conversion
  Dear all, I used the Galaxy tool to convert the .gff3 annotation file to .gtf format. Going thro...
• salmon gene quant to DESeq2
  Hi again - I successfully ran salmon on my fastq files, including gene-level summary via a simpl...
• Cufflinks error when trying to align against genome
  I am working with tophat2 and cufflinks in order to try to align RNA-seq reads against an assembl...
• DESeq2 file missing
  Hello everyone, I tried to use DESeq2 2015-10-14 (owner iuc) from the toolshed. Unfortunately it...
• Deseq2 transcript list classification
  Hi everybody, I did RNA-seq on mouse stem cells and i got a list of differentially expressed tran...
• Deseq2 error running R script
  Hi, I am having problems in running deseq2 package in my local galaxy installation. It says R bro...
• Error - Heatmap generation / visualization from RNA-seq data using DESeq2 workflow
  Hi I wanted to try generating heatmaps of gene expression using normalized counts file obtained ...
• StringTie and StringTie merge - when to apply the Guide gff (reference annotation file)?
  I'm new to StringTie and I've been trying following the "Finding and quantifying new transcripts"...
• Nebula Problem
  Hello, I'm using Nebula and when I try to use the annotation tools (genomic annotation and gene ...
• Creating StringTie output that meets DESeq expected input content for DE analysis
  Good Morning, Since StringTie can produce output files for differential expression that can be us...
• DESeq2 Fatal Error (undefined)
  I'm trying to run DESeq2 on one factor with two levels and I get the follow error message: Fata...
• Fw: Error In Annotation Tools
  I edit: Actually I can´t do anything in nebula server, even upload data, I got the cluster error...
• Stringtie Deseq2/EdgeR count tables all zero
  Dear Galaxy Team, I encountered a different problem with Stringtie + output additional files for...
• Error with DESeq2 with Kallisto abundance.tsv input
  Hello everyone, I'm trying to run DESeq2 (Galaxy Version 2.11.40.2) on Kallisto abundance.tsv dat...
• Error in DESeq2
  Hello, I'm trying to run a DESeq2 analysis of my ten RNASeq Samples. I successfully was able to ...
• DESeq2 Error on Cloudman
  Hi I'm working on Cloudman doing RNASeq transcriptome analysis. I've made BAM file using TopHat2...
• Stringtie tool failed with error "NameError: name 't_id' is not defined"
  Hello I have used the Stringtie tool successfully to produce transcript assemblies and additiona...
• Cuffdiff Errors: "Loading reference annotation" and "Inspecting maps and determining fragment length distributions".
  Hey, I have 30 individuals that have two samples each. I've had no problem running Cuffdiff bet...