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• Cuffdiff Errors
  Hello, I am having a problem running Cuffdiff on some RNA-seq data. I want to compare 2 sampl...
• Error Running Cufflinks
  Dear Jen, after a couple of days of running cufflinks on a sam file (data 9) with an annotated r...
• Cuffdiff Failed
  Hi, I had 3 samples (2replicates treated (A-B) and one untreated (C) ). I did cufflnks and cuff...
• HTSEQ count error
  Hello, This is my first rna-seq data analysis project and I am using Galaxy to analyze different...
• sam to bam - Galaxy version 17.01
  Hi All First of all I am not a bioinformatician, I'm looking at someone else's test workflow. I ...
• Installing HISAT2 on Cloudman
  Hi Galaxy, I am trying to install HISAT2 from the toolshed to my Cloudman instance (revision da2c...
• Error In Tophat
  This is the error I am getting while running Tophat. What's causing this? I have the default hg19...
• Mapping Mirna Data
  Dear All I am interested in using Galaxy to compare miRNA sequencing data. I have previously gr...
• Sam Filtering And Header/Sorting Issues
  Dear All, I would like to add some filtering steps in my RNA-Seq pipeline. To do so, I used the a...
• Cuffdiff Error on Galaxy??
  Hi, I am trying to run cuffdiff on Galaxy and I keep on running into the same error: Fatal error...
• quantifying differential gene expression across three groups using cuffdiff
  Hello, I am trying to identify differentially expressed genes across three groups.  The groups c...
• Cuffdiff Fatal error: Exit code 1 () Error: number of labels must match number of conditions number of labels must match number of conditions
  Hi! I ran into a problem using Cuffdiff. (I am using a local version of galaxy). When I try to ...
• Cufflinks Error With Illumina Igenome .Gtf For Annnotation
  Hi all, I am attempting to use tophat>cufflinks>cuffmerge>cuffdiff to compare transcri...
• Cuffdiff error- Fatal error: Exit code 139 ()
  Hi, I am getting the following error while running Galaxy cuff diff. An error occured with t...
• Bowtie with -a --best --strata does not seem to limit alignments to the best strata
  I am using bowtie for illumina on the NGS Galaxy public server. This is the code for the run tha...
• bowtie2 out of memory
  I'm trying to run bowtie2 in galaxy on my own centos installation to align paired end data to the...
• Analyzing Rna-Seq Replicates Using Cuff(Links/Compare/Diff)
  Hello! I have 10 human RNA-Seq samples consisting of 3 groups (2 replicates per ...
• HTSeq-count, maximum buffer size exceeded
  Hi all, I am new of RNA-seq analysis. I am running HTSeq-count on galaxy with defaut parameters....
• Galaxy RSEM error
  Dear all,   I am trying to run RSEM via Galaxy but there is a problem. FYI, 1. Reference sequ...
• Problem With Running Cufflinks
  Hi everyone, After mapping my RNA-seq data to the reference transcriptome using Bowtie, I trie...
• 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...
• Problems With Tophat
  Hello, I have successfully used the public server for processing RNAseq data but I have run into...
• Workflow Failure Issue with .dat Compressed Files on a Local Galaxy Instance
  Greetings, We have developed a workflow using a local galaxy server instance including the follo...
• 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...