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• Cuffmerge error - how to fix it
  Hi guys, I am doing cuffmerge with reference annotation on my files after cufflink. The error oc...
• 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 "Matched on error" - Check for problematic input format
  Hi, This is my first time analyzing RNASeq data. I mapped and aligned my reads using tophat and...
• Merging BAM files: bamtools not found
  I have BAM files from aligning paired end Illumina reads. I would like to merge the aligned seque...
• Iterative Mapping -> open: No such file or directory
  Hi, when I try running "Iterative Mapping" I get the following error. Please help! Usage: ...
• Fatal error :Exit code 1
  Am getting the error below with "NSG: Picard:" and am using the tool "fixmate information". What ...
• Extract Genomic DNA error with custom genome
  Hi, I'm new to Galaxy, and I and trying to use the "extract genomic dna" tool. I would like to f...
• 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...
• mapping NGS data with BWA for Illumina
  Hello!   i am trying to map single-end reads using BWA for Illumina but an error accoured: Er...
• htseq-count error with strand data
  Hi! I am running htseq-count for a RNA-seq and I got this error: Fatal error: Unknown error occ...
• BAM files cannot be downloaded and failed MergeSamFiles Fatal error: Exit code 127 ()
  Hi, I've mapped some WES and WGS data through the pipeline. For the past two days, either the "m...
• having problem with GATK
  I am Bhagyashri and i have problem using GATK tool in GALAXY. I am getting this error mentioned b...
• picard collectwgsmetrics error
    Hi..I am trying to use the picard collectwgsmetrics on a bam file generated from a whole genom...
• Question: SAM-to-BAM: fatal exit code Error 139
  Dear All, I am analyzing DNAseq data. I obtained a SAM file by using "Map with BWA for Illumina ...
• Reference Annotation Sources for RNA-seq tools
  When running htseq count, I got this error message: Fatal error: Unknown error occured [bam_...
• Help with using the multiBam Summary tool - error message
  Hello, I have just aligned some reads using Bowtie2 and am wanting to look at correlation betwe...
• How to use cuffmerge and cuffdiff
  I am trying use Galaxy to analysis the yeast RNA-seq data. When I want to try the cuffmerge and c...
• Cuffmerge ValueError merging assembled transcripts
  I am attempting to analyse my first RNA-seq experiment using Tuxedo tools. When I attempt to cuf...
• DeepTools plotCorrelation Error "IOError: [Errno 22] Invalid argument"
  Dear all, I used a matrix generated from multiBamSummary to run plotCorrelation but the error m...
• htseq-count unknown error
  I am trying to use htseq-count tool for gene quantification, but I have this error: **"Fatal err...
• BAM files fail to be recognized
  I generated BAM files on galaxy using BWA-MEM. I am trying to run BAMtools, Picard, etc on them. ...
• GATK: Unified Genotyper Error
  Greetings, I get the following error when running the GATK's Unified Genotyper using default set...