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• 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 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...
• Running SnpEff on Galaxy
  Hello, I would like to annotate a .vcf file and also summarize possible effects variants can hav...
• What Galaxy tools can preprocess VCF file before running the SNPEff annotation process?
  What Galaxy tools can preprocess VCF file before running the SNPEff annotation process? We have t...
• 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...
• What Galaxy tools can substitute VTTools for preprocessing VCF file before the SNPEff data input?
  What Galaxy tools can substitute VTTools for preprocessing VCF file before the SNPEff data input?
• SnpEff C.elegans reference
  I am trying to annotate a vcf file with SnpEff for C.elegans genome. Could you please show me how...
• How to use ANNOVAR with bacterial genome?
  I am trying to automatically generate annotations for a VCF file generated from the Mtb H37Rv gen...
• Htseq-count input data
  Dear colleagues, I am a new Galaxy user motivated to exploit its tools to compare two sets of the...
• Tuxedo_Custome build genome
  I have uploaded tomato genome in GFF3 and FASTA format in galaxy. However, when I run Tuxedo, my ...
• RNA Star problems
  I am pretty new in Galaxy. I have been following some tutorials in order to perform some DEG with...
• 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...
• SnpEff supports only genomes of two species?
  Under usegalaxy, I was trying to use SnpEff to annotate my VCF, but the genome dropdown list show...
• What does "WARNING: All frames are zero! " mean and how to fix it when using SNPEff?
  What does "WARNING: All frames are zero! " mean and how to fix it when using SNPEff?
• gtf file error
  Dear all, My reference genome is Duck, not index in Galaxy reference genome. So i downloaded fast...
• Problem with collectrnaseqmetrics (Galaxy)
  I am attempting to run CollectRnaSeqMetrics on a tophat run (with my gff3 annotations and fasta g...
• Empty data result from Cufflinks
  Hi I am trying to run Cufflinks on some BAM files that I have generated using HISAT2 with upload...
• Gene annotation dataset from Ensembl not recognized by Cufflinks
  Hello Galaxy/Biostars, I am trying to perform RNA-seq analysis using Cufflinks at Galaxy. In ord...
• annotations with genome of reference
  hi, Dears I am working with RNA-seq and i dont understand how create a de novo transcriptome usi...
• Cufflinks Related Problem
  Dear Noa, Can you please tell me the parameters that I should keep while mapping bacterial tran...
• SnpEff error and problems downloading genome
  Running SnpEff generates the following error: Fatal error: Exit code 1 (Error) Picked up _JAVA_OP...
• How to annotate 500 vcf files using SNPEff or smth else and put every separate result in a folder with the name of the SRA identifier?
  How to annotate 500 vcf files using SNPEff or smth else and put every separate result in a folder...