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• GTF file is not recognized
  Hello, I am trying to align my hits with a GTF file that I upload from Ensembl, however it is no...
• GATK Select Variants Reference Genome
  Hi, I'm trying to use GATK Tools Select Variants on VCF files of whole genome sequencing data, ...
• featureCounts doesn't recognize Rat annotation file in history, what am I doing wrong?
  Dear Experts, I use Htsat2 output file for running feature-counts, but when I set up the run Gala...
• galaxy doesn't recognise dbSNP file I uploaded
  Hi I'm somewhat new to the game and struggling with the GATK unified genotyper. I found a dbsnp...
• DBSNP, Variant Caller
  I have a VCF file from FreeBayes Variant caller. However I want VCF file to have dbSNP (rsID). T...
• Why won't Galaxy recognise uploaded hg19 .fasta.gz file?
  Hi. I'm doing RNA-seq analysis for the first time and want to upload the hg19 genome from 1000 Ge...
• Need help with "Filter by quality" tool
  Why doesn't this tool recognize my fastq files? It won't let me run the tool on the fastq files I...
• Problem running BWA-MEM mapping
  I am trying to run BWA-MEM mapping in galaxy. I have uploaded FASTQ files using fastqcssanger and...
• Where to get SNPs and Indels?
  I downloaded some files from Broad Institute but Realigner Target Creator won't work with these f...
• using SAF gene annotation file in featurecounts
  Hello! I'm new to Galaxy and was wondering if I could get some help with using the featurecounts...
• Convert genome coordinates from hg38 to hg19
  I think I have done this before and it worked perfectly, a few weeks ago, but somehow I can't get...
• Snp Calling Problems
  Dear all, I have been looking for an answer to my problem in all the Galaxy Support resources bu...
• Wig/BedGraph-to-bigwig converter doesn't recognize my bedGraph file - why?
  Hi, Am new to Galaxy but has successfully converted a number of downloaded Wig files to bigWig f...
• Variant mapping workflow and tutorial in Galaxy
  Hi, I have a zebrafish mutant that I am trying to map. So I did the mapping crosses and sequenced...
• can't get any VCF tools to work
  Hi, I can't seem to get any of the VCF tools to work on my combined VCF file, can't sort it, can'...
• MACS2 input not recognized by tool
  Hi all, I've been using Galaxy to analyze my ChIP-seq data, and have managed to get the program ...
• Need help with "Unified Genotyper" tool
  Hi there, I would like to add the file 'dbsnp_137.hg19.vcf' to my GATK unified-genotyper analysi...
• Snippy does not recognize my genbank reference file
  Hi, I'm using snippy to look for SNPs in my bacterial genomes. Snippy does not seem to be able t...
• BAM doens't upload properly
  Hello I am having some problems with uploading my BAMs. After uploading it says that it is still...
• file ARFF not recognized in my history
  Hi there, I am trying to upload an ARFF file to https://galaxy.cbio.mskcc.org to use the SVM Too...
• Data Library Import "Tool Error"
  Hi, I used the "Upload files from filesystem paths" option to upload a directory path in...
• Need help with "FASTQ Quality Trimmer" tool
  I have uploaded .fastq files successfully but the "FASTQ file" drop-down list doesn't show my .fa...
• Help! I'm using trimmomatic in Galaxy, but it doesn't recognize a part of input dataset.
  I'm using Trimmomatic to trimming paired end reads. When I set "Single-end or paired-end reads?"...