Similar posts • Search »

• 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...
• Galaxy GEMINI database version == GEMINI release?
  GEMINI includes hardcoded database versions in its build procedure. GEMINI on Galaxy seems to con...
• Loss of original VCF file; therefore in Galaxy, can I use VCF manipulation on an excel file (originally converted from VCF format)
  I have inherited a project where the original VCF files were lost. I have the excel files derived...
• 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...
• DBSNP, Variant Caller
  I have a VCF file from FreeBayes Variant caller. However I want VCF file to have dbSNP (rsID). T...
• Realigner target creator
  Hi I am trying to use realigner target creator in Galaxy, however the tool is not recognising hg...
• Installing Gemini tools
  Hi, I'm trying to install the Gemini tools on a local galaxy instance (release 17.05) and am run...
• fatal error exit code 1 from Trimmomatic when input fastq data has an incorrect datatype assignment
  trying to run my dataset with trimmomatic I have changed the files to fast-q-sanger, but it isn'...
• Conversion of a .vcf (variant control format) to a .maf (mutation annotation file)
  Hello, Is there a galaxy package which will convert a .vcf to a .maf (mutation annotation file)?...
• Intersect more than two vcf files
  Hi everyone, I have nine vcf files that I'd like to intersect. I want to know which, if any, gen...
• Trouble With Blast+ And .Loc File
  Dear Galaxy users, I have been trying to upload a blastable database in my local instance of...
• Fwd: Exome Sequencing Analysis
  Hello, My name is Johnathan Cooper-Knock, I am a clinical fellow based at the University of Shef...
• galaxy generated bigwig files won't load from GEO
  I generated bigwig files on Galaxy which display nicely on the USCS browser via the direct link f...
• How to intersect vcf files for commonly mutated genes only (not the exact mutation)
  Hi all, I intersected two vcf files using vcf-vcf intersect on usegalaxy.org and I realized that...
• Mpileup with vcf output?
  Hello, I noticed that the "mpileup" tool that gives an output file in vcf format is no longer av...
• Gff3 not recognised by cufflinks
  I am trying to use cufflinks, but it does not recognise my reference annotation.  I have a gff3 f...
• VCF file samples not called
  I'm trying to identify polymorphisms in three samples. When I get the VCF file there are many var...
• Problem Mapping 454 Reads In Fastq Format Using Lastz
  Dear Galaxy Team and users, I have some 454 reads that I would like to map against a contig asse...
• Why Is 'Filter Pileup' Not Recegnising My 'Generate Pileup' File?
  Hi, I was wondering if you could help me with a problem I have been having recently. I have ca...