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• Gene Names From Cuffdiff Data
  How does one get gene names when using cuffdiff when looking at "gene differential expression tes...
• Get generic rather than specific gene names
  I have a gene output from some differentially regulated arabidopsis and genome and want to run i...
• Help with interpreting RNA-seq output
  I am new to galaxy and have been trying to figure out how to align RNA-seq reads to a genome in o...
• Tophat Mapping And Cufflinks Output Issues
  Hello Galaxy Users- I've been using the Main Galaxy server to work on an RNA-Seq project for a n...
• Output Files of MACS2 bdgdiff
  Hello everyone, I have some bedgraph files from a ChIP-Seq experiment (2 replicates for each cond...
• Is Tss_Id Unique For Each Transcript?
  Dear All, I am reading and comparing the outputs of Cuffdiff. I found there is a "tss_id" column...
• DAVID creates an empty link
  I try to work with DAVID, but I don´t know if the problem is with the identifier type, or any oth...
• Integrate pipeline chain of apps with multiple output files
  I wrote a pipeline, a set of apps in Python. Every app outputs thousands of files. Every app will...
• Encountered message from UCSC: "Reached output limit of 100000 data values"
  Hello, I am a green hand in using Galaxy. I have got two tables from UCSC, one is about the miR...
• Rna-Seq Analysis
  Dear all, I am using Galaxy for RNA-Seq analysis. I expect two lists: differentially expressed tr...
• salmon gene quant to DESeq2
  Hi again - I successfully ran salmon on my fastq files, including gene-level summary via a simpl...
• Rna-Seq Analysis
  Since the pictures are too big for the mailling list. I will upload it in seperate emails. Dear ...
• gene Symbol from cuffdiff output
  Hi. I received output from cuffdiff which included gene_id, gene and locus for each differential...
• Is it possible for workflow parameters to take information from the names of input datasets? e.g. ${Read_group } is set to be the first three characters of input dataset name.
  HI. I would like to run a workflow in parallel on list of  multiple data sets (using the dataset ...
• Cuffdiff 2.2.1.5 error with cummeRbund SQlite. "Fatal error: Exit code 1 () -- use version 2.2.1.3 instead
  Hi, so as a disclaimer, I am very new to RNA seq analysis. I received the following error while r...
• cufflinks splicing analysis drosophila - 'notest' in output
  Hi everyone, I'm attempting to use cufflinks to examine alternative splicing in my RNAseq data f...
• Problems With Picard And Gatk Tools
  Dear all, I have been trying to analyze some recently acquired WGS reads (re-sequencing with MiS...
• Gene And Transcript Names From Cuffdiff
  Hi all, I am learning how to use Galaxy to analyze my RNA-Seq data. After running cuffdiff, one ...