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• 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...
• salmon gene quant to DESeq2
  Hi again - I successfully ran salmon on my fastq files, including gene-level summary via a simpl...
• DESeq Duplicated Row Names Error
  Have you experience a similar error like this in Galaxy?: Fatal error: An undefined error oc...
• How to solve DESeq2 error
  For RNA analysis, I finished TopHat , HTseq-count. But When I run DESeq2 for two groups, error ca...
• error in iep
  I would like to report an error in iep: Devices allowed (with alternative names) are:- ps (posts...
• 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...
• Problem with Annotation Regions using ANNOVAR Annotate VCF
  Hello, I'd like to use ANNOVAR Annotate VCF via Galaxy Web (Galaxy Version 0.2) to annotate vari...
• Cummerbund visualization of expression plot
  I am following the NGS101-16 video on Cuffdiff/Cummerbund to learn how to use Cummerbund. For ex...
• 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 ...
• September 8, 2010 Galaxy Development News Brief
  September 8, 2010 Galaxy Development News Brief http://bitbucket.org/galaxy/galaxy- central/wik...
• Is it possible for a tool to scan all the files in its history when it's run?
  I'd like to be able to inspect a history from within a tool, but I don't see an easy way to deter...
• Principal Component Analysis
  Hi, When I'm running Principal Component Analysis in GALAXY it gives me error: Encountered erro...
• Bad Value For -Sequence With -Auto Defined
  I have been importing fasta files into galaxy then attempting to GetOrf on these files.  I have b...
• HTML output issue with FastQC on a local Galaxy
  Does anyone also having problem with html output in Galaxy ? I am getting raise Exception('Un...
• Using value from file in when condition in galaxy xml
  Hi everyone, I started to use the option from_data_table in xml file instead of from_file as it ...
• Error when running Bismark with pair end/Full parameter list
  Hi, When trying to launch a Bismark with bowtie2 I get the following error: Error executing too...
• HELP!! BAM file shows one line analysis with zero values when "bam coverage" is run
  Hi I have uploaded four BAM files to the galaxy. I ran BAM coverage on them with 100 bin. One fi...
• Cufflinks generated duplicated features
  Hi everyone i post my situation because i have this error: > GFF Error: duplicate/invalid 'tr...
• Duplicate row name error using Limma
  Hi, Trying to run limma on Galaxy. After downloading my files, which contain gene IDs, I get thes...