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• 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...
• How to solve DESeq2 error
  For RNA analysis, I finished TopHat , HTseq-count. But When I run DESeq2 for two groups, error ca...
• error message when running Deseq2 on featureCounts output files
  I get the following error message when running Deseq2 on two samples (tumor and normal) that was ...
• htseq-count issues with Deseq2
  This is the first time im trying this but I keep running into issues. I'm running the htseq-count...
• Problems with analyzing fastq to fasta files using DESeq2
  I need help please. I uploaded Fastq converted to Fasta data to Galaxy and started the DESeq2 pro...
• 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...
• Fatal error with DESeq2 when processing TPM-based Salmon files and using a tabular transcript-gene mapping file
  Hi there, I have used Salmon to map RNAseq reads to a transcriptome. I then proceeded to anal...
• Running DESeq2 inside local Galaxy instance
  We have tried many times to install DESeq2 to our local instance of Galaxy. The install is succes...
• salmon gene quant to DESeq2
  Hi again - I successfully ran salmon on my fastq files, including gene-level summary via a simpl...
• Error in DESEQ2
  I am obtaining the following error while working with DE-seq2: Fatal error: An undefined err...
• DESeq2 Fatal error
  I am using DESeq2 to find deferentially expressed genes from count tables. My Input files are fe...
• Tool problems when using older versions of downsampled tutorial data
  Hi, I'm a newbie in Ref-seq and I'm trying to make a pipeline using HiSat -> HtSeq -> DESeq...
• DEXseq error - "Error in library("DEXSeq") : there is no package called 'DEXSeq'"
  Dear all I want to analyse my RNA-seq data using DEXseq on the galaxy platform. I have made count...
• 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...
• DiffBind problem on Galaxy
  Hi, I am using Diffbind and get the following message: [1] "en_US.UTF-8" Fatal error: An undefin...
• Deseq2 RIP seq analisys
  I am following this: https://support.bioconductor.org/p/61509/ After HTseq, Deseq2 cannot perfor...
• STAR in multiple threads faces issues in opening genome file
  Hi, I'm running STAR with multiple threads in multiple cores and for some samples I get an error...
• Diffbind and repmatch fatal error
  Hi! I have 3 chip replicates and I want to find common peaks within them. I used diffbind to do s...
• Cuffdiff crashing suddenly
  Hello, I'm running cuffdiff and this error comes up when it runs. Fatal error: Matched on e...
• DESeq Duplicated Row Names Error
  Have you experience a similar error like this in Galaxy?: Fatal error: An undefined error oc...
• download.file function error
  Hello, I have been trying to wrap R-based tool to download data from GEO database and I have trie...
• DESeq2 file missing
  Hello everyone, I tried to use DESeq2 2015-10-14 (owner iuc) from the toolshed. Unfortunately it...