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• On executing SnpEff n a Galaxy cloud instance we have the error: All frames are zero
  On executing SnpEff we have the following error: WARNING: All frames are zero! This seems rather...
• How to fix SNPeff`s error "WARNING: All frames are zero! "?
  After execution of the job for processing of the normalized with VT Tools Pilon`s VCF file we h...
• How to normalize and decompose a VCF file using only Galaxy-available tools?
  How to normalize and decompose a VCF file using only Galaxy-available tools? The goal is to make ...
• How to preprocess .fasta genome reference, .gff3 annotation file and the input VCF to escape from the Frame Zero error with SNPEff?
  How to preprocess .fasta genome reference, .gff3 annotation file and the input VCF to escape from...
• Error Using MAFFT
  I was trying to run MAFFT of two data sets, but it said error because the job was "cancelled by a...
• Snpeff - Reports Gain Of Stop Codon As Frame_Shift In Some Cases
  Hi Pablo, Correct me if I am wrong, but I believe that SNPEff doesn't check the inserted sequenc...
• snpEff gene names
  Hello! I am new to snpEff. I built my database for my sample using gff3 files created from PROKK...
• cufflinks running problem
  Hello, I´m having problems in running Cufflinks. Yesterday morning I used the Tophat accepted hi...
• When running SNPEff on Galaxy on the normalized with VT tools VCF with M. Tuberculosis genome we have: WARNING: Chromosome 'gi|559794742|gb|CP003248.2|' not found
  When running SNPEff on Galaxy on the normalized with VT tools VCF with M. Tuberculosis reference ...
• Use Own Junctions Or Not
  Dear All, I want to compare the pre-mRNA alternaive splicing events between RNA- seq datasets. S...
• Issues with Using CuffDiff Tool in Galaxy
  Hi,   I am analyzing microRNASeq data. My pipeline is qc reads, bowtie for alignment, cufflinks...
• Genome source from history in SnpEff
  Hello, I am using SnpEff in Galaxy to add variant information to my vcf file. Please let me ask 2...
• zero fpkm value in cufflink
  hi i have done cufflink on my sra seq according to the ngs pipeline. the result says fpkm value...
• Couldn't resolve host 'usegalaxy.org'
  Hello. I tried to export datasets from usegalaxy.org to our local server. I followed the follow...
• SnpEff database build tool for C.elegans
  I am trying to use the SnpEff build database tool to build reference genome for C.elegans and use...
• Fatal error :Exit code 1
  Am getting the error below with "NSG: Picard:" and am using the tool "fixmate information". What ...
• mpileup warning and problem with bcftools call
  I am using mpileup and bcftools call in Galaxy. Mpileup produces a VCF output file, but also give...
• Need help with "SnpEff" tool
  hi i am trying to use snpeff on galaxy...i give vcf file but i dnt know in genome portion what i ...
• SnpEff fails to add expected annotation when run at http://usegalaxy.org
  what is the meanning of none in the table of Number of effects by type and region, thank you very...
• How to set up SNPEff jars and tools on the Galaxy cloud instance?
  On running various SNPEff tools we have got: Error: Unable to access jarfile /home/pcingola/too...
• Tool problems when using older versions of downsampled tutorial data
  Hi, I'm a newbie in Ref-seq and I'm trying to make a pipeline using HiSat -> HtSeq -> DESeq...