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• What to do with Cuffquant .cxb files
  I would like to get a raw RNA-Seq counts matrix from the results of the Tophat alignment to a ref...
• Normalization of RNA-seq data
  Hi, I am wanting to normalize my RNA-seq data without running a differential gene expression on...
• HT-SEQ and edgeR installation
  Do you have HT-seq  and edgeR tools installed in Galaxy. If I want to get one, is it possible to ...
• To merge several count data into one matrix.
  Hello all. I would like to merge or combine my count data into one matrix for using Degust prog...
• I am slightly confused about the input requirements for the differential expression tool - last step of Trinity
  Hello all, I have a pressing question... To start with, I have read the Trinity methods paper ...
• Bowtie Raw Input
  Hi There Im trying to map RNA-seq data to a reference genome in Galaxy (Main instance) using bot...
• HTSEQ count error
  Hello, This is my first rna-seq data analysis project and I am using Galaxy to analyze different...
• Extracting Raw Count Data From Mapping
  Hi, I would like to extract raw counts from tophat output. Does anyone know a way to do this in...
• voom normalized count data matrix (Differential count 0.3.0)
  Hi, I have used voom from the "Differential count" package and it worked smoothly. I would like t...
• RNA-Seq raw count data analysis using GALAXY
  Hi, I have downloaded the raw_readcounts files (.txt files) from an RNA-Seq experiment using GSE ...
• Galaxy Main unable to load files into history uploaded by FTP (and other general flakiness the past few days)
  Hello, I uploaded several RNA seq raw reads via FTP without any issues, but I have been unable to...
• Replicate Common Gene Names
  This is somewhat Galaxy related, but more of a general question. I did all of my mapping and ini...
• Raw Count Of Genes
  Dear all, I am a Phd student working on chicken genomics, with limited experience in the bio-inf...
• Cuffdiff error- Fatal error: Exit code 139 ()
  Hi, I am getting the following error while running Galaxy cuff diff. An error occured with t...
• sam to counts in toolbox
  I am trying to run DEseq with my rna seq data.  I am following the tutorial "http://training.bio...
• Deeptools compute matrix
  I love Deeptools, and so glad that galaxy has moved them to the main server. It's awesome! I can...
• Galaxy app to retrieve selected raw reads
  There are many previous threads regarding how to retrieve selected raw reads from fastq files off...
• Raw Counts From Galaxy
  Dear all, I would like to analyse some RNA-Seq I obtained in the chicken. I am implemented the...
• How to update the tool menu
  Sometimes I want to move tools around within the tool list/menu that appears in the left hand col...