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• TopHat: Error: Couldn't build bowtie index with err = 1
  Hi I'm trying to run TopHat on a Cloudman Galaxy instance and I keep getting the below error. I'...
• RNA Star problems
  I am pretty new in Galaxy. I have been following some tutorials in order to perform some DEG with...
• Galaxy cloud instance won't initialize
  Hi Galaxy Team,   I am in desperate need of using the cloud so that I can analyze by rather lar...
• Tophat in usegalaxy
  Hi, I'm running galaxy in usegalaxy, I got these error. Previously I was running tophat in ami (...
• usegalaxy build snpEff database via genbank
  Hello, I have built the SnpEff4.3 database for Salmo salar's chromosome 25 from Genbank and I hav...
• VCFFilter 1.0.0 fatal error with FreeBayes VCF input
  When running a vcf file (output was from FreeBayes tool), I am getting the fatal error Fatal...
• Reference annotation GFT GFF3 problem with tool HISAT
  I got the following error while running htseq count: I think it is my gtf file problem. How to fi...
• Problem with HISAT
  Hi, Im trying to run a custom workflow for RNA-seq data structured as follows: 1. Inputs: refer...
• Snpeff build error
  Hi, I am trying to do exome analysis among Solanum lycopersicum leaf curl mutants. I have follow...
• Cuffdiff error- Fatal error: Exit code 139 ()
  Hi, I am getting the following error while running Galaxy cuff diff. An error occured with t...
• Problem with TopHat in Galaxy using data from Nature Protocols
  Hi, I am a graduate student who began RNA-seq data analysis recently. I am having a trouble with...
• Building Bowtie index, failed
  I encountered a problem when trying to mapping RNA-seq reads to the genome. Fatal error: Tool ex...
• Erorr with runing cuffmerge
  Hello I am doing RNA-seq analysis, I am trying to run cuffmerge for assembled transcripts files...
• Cuffmerge fails to merge gtf files
  Hello, I am trying to merged to assembled transcripts produced by cufflinks using cuffmerge. I ...
• TopHat Fata Error: Fusion search fails with Bowtie2, how to try Bowtie1 option? Also truncates file during genome alignment
  I am trying to run TopHat using a GTF annotation to build a transcriptome index, and also search ...
• DeepTools plotCorrelation Error "IOError: [Errno 22] Invalid argument"
  Dear all, I used a matrix generated from multiBamSummary to run plotCorrelation but the error m...
• STAR: command not found
  Hi, I am trying to run RNA STAR from the galaxy platform and I get the following error: /galax...
• RNA star fails on collection
  Using RNA-Star on collection now results in the job "succeeding" but all alignments are empty and...
• Unknown error on HTseq_count
  Hi, I’m trying to do RNA_seq analysis with Galaxy. I upload the hg38 iGenome from illumina to my ...
• Tophat
  Hi, I am running galaxy locally and when I perform alignments with TopHat I get the following ...
• Problem merging five 13.9 GB .BAM files
  I keep getting this error when I try to merge five 13.9 GB .BAM file. Any ideas on how I can get ...
• Cuffmerge error - how to fix it
  Hi guys, I am doing cuffmerge with reference annotation on my files after cufflink. The error oc...
• Error in Extract Reads
  Get this error when trying to execute the program "Extract Reads" in Galaxy. For the input, I us...